Intro

suppressPackageStartupMessages({
  library("reshape2")
  library("kableExtra")
  library("dplyr")
  library("RColorBrewer")
  library("GenomicRanges")
  library("limma")
  library("methylKit")
  library("gplots")
  library("seqinr")

  library("liftOver")
  library(rtracklayer)
  library(GenomicFeatures)
  library(ggbio)
  library(Homo.sapiens)

})

Notes

Pool1 and pool1 data were merged before analysis.

There is some data named pool14b which was changed to pool14.

My notes from our meeting yesterday:

  • Percent CpG sites with usable data (done)

  • Just provide the beta values (done)

  • remove pool8, pool17 and rerun stats

  • Adjust by bisulfite conversion

Off target reads

DATADIR="fastq"

oft_name = paste(DATADIR,"/3col_offtarget.tsv",sep="")

oft <- read.table(oft_name)

x <- t( as.matrix(acast(oft, V2~V1, value.var="V3")) )

x <- x[,which(colSums(x)!=0)]

x %>% kbl() %>% kable_styling()
Assigned Unassigned_Ambiguity Unassigned_NoFeatures Unassigned_Unmapped
101-1023 6 1 56303 54
185-1135 40 1 49810 13995
7185 3 2 41439 33
Neg 0 0 0 0
NTC 0 0 0 0
pool1 38090 8382 40957 25941
pool10 12517 5445 30254 322
pool11 1704 792 2644 100
pool12 30597 7399 32159 6516
pool13 13353 6554 28072 23124
pool14 12107 6142 26051 482
pool15 13567 5653 23714 5248
pool16 16359 8168 29394 353
pool17 12111 5581 18616 2693
pool18 13331 6023 18734 4482
pool19 21994 8436 28257 1705
pool2 10500 8811 30452 7882
pool20 6164 3661 13226 1856
pool21 24421 10121 31503 358
pool22 13533 9907 31076 7665
pool23 13910 8316 21453 2354
pool24 16840 6651 19216 5263
pool3 11142 6649 29355 8899
pool4 12702 9295 26499 4232
pool5 14707 8075 27974 13020
pool6 18355 11346 43979 841
pool7 10369 5997 25080 16083
pool8 10254 7360 38729 10582
pool9 12772 6327 20104 7550
PoolM 35540 9028 46861 617
PoolMM 29923 6924 42942 1431
Undetermined 24291 10479 59327 75519
xx <- t(x/rowSums(x) * 100)

t(xx) %>% kbl() %>% kable_styling()
Assigned Unassigned_Ambiguity Unassigned_NoFeatures Unassigned_Unmapped
101-1023 0.0106451 0.0017742 99.89177 0.0958058
185-1135 0.0626508 0.0015663 78.01585 21.9199323
7185 0.0072329 0.0048219 99.90838 0.0795622
Neg NaN NaN NaN NaN
NTC NaN NaN NaN NaN
pool1 33.5979536 7.3934903 36.12684 22.8817147
pool10 25.7880424 11.2180148 62.33055 0.6633978
pool11 32.5190840 15.1145038 50.45802 1.9083969
pool12 39.9068748 9.6503241 41.94415 8.4986501
pool13 18.7797983 9.2176139 39.48075 32.5218345
pool14 27.0354160 13.7153321 58.17293 1.0763253
pool15 28.1578183 11.7325972 49.21755 10.8920344
pool16 30.1415042 15.0495633 54.15853 0.6504035
pool17 31.0530499 14.3098895 47.73211 6.9049512
pool18 31.3154804 14.1484614 44.00752 10.5285412
pool19 36.4187310 13.9687376 46.78931 2.8232216
pool2 18.2149362 15.2849336 52.82678 13.6733455
pool20 24.7480628 14.6986791 53.10154 7.4517204
pool21 36.7769528 15.2417812 47.44213 0.5391323
pool22 21.7638829 15.9325196 49.97668 12.3269166
pool23 30.2174527 18.0653010 46.60352 5.1137228
pool24 35.1052741 13.8649156 40.05837 10.9714405
pool3 19.8804532 11.8636810 52.37755 15.8783121
pool4 24.0896677 17.6282051 50.25603 8.0260962
pool5 23.0603989 12.6615028 43.86290 20.4152032
pool6 24.6306410 15.2252385 59.01558 1.1285409
pool7 18.0239531 10.4243077 43.59540 27.9563351
pool8 15.3216287 10.9973851 57.86926 15.8117295
pool9 27.3180331 13.5328214 43.00045 16.1486963
PoolM 38.6111292 9.8081394 50.91041 0.6703170
PoolMM 36.8419109 8.5249938 52.87121 1.7618813
Undetermined 14.3211725 6.1780728 34.97724 44.5235119
par(mar=c(5, 10, 5, 2))
barplot(rowSums(x),horiz=TRUE,las=1,cex.names=0.7,main="total reads") ; grid()

barplot(x[,1],horiz=TRUE,las=1,cex.names=0.7,main="assigned reads (on target)") ; grid()

barplot(x[,2],horiz=TRUE,las=1,cex.names=0.7,main="unassigned reads (ambiguity)") ; grid()

barplot(x[,3],horiz=TRUE,las=1,cex.names=0.7,main="unassigned reads (off target)") ; grid()

barplot(x[,4],horiz=TRUE,las=1,cex.names=0.7,main="unmapped reads ") ; grid()

par(mar=c(5, 10, 5, 2))
barplot(xx,horiz=TRUE,las=1,cex.names=0.6,xlab="proportion of reads (%)", 
  legend.text=TRUE,
  args.legend = list(x = "topright" , bty = "n", inset=c(0, -0.15), cex=0.8))
  grid()

barplot(xx[1,],horiz=TRUE,las=1,cex.names=0.7,main="proportion of reads on target (%)") ; grid()

On target reads

ont_name = paste(DATADIR,"/3col_ontarget.tsv",sep="")

ont <- read.table(ont_name)

y <-t( as.matrix(acast(ont, V2~V1, value.var="V3",fun.aggregate=sum)) )

y %>% kbl() %>% kable_styling()
LEP NPY_1 NPY_2 POMC_1 POMC_2 SOCS3 TNF
101-1023 0 0 0 0 2 0 4
185-1135 4 0 0 1 23 6 6
7185 0 0 0 0 1 0 2
Neg 0 0 0 0 0 0 0
NTC 0 0 0 0 0 0 0
pool1 192 9 7 16802 13978 3930 3172
pool10 1117 10 10 253 5316 4993 818
pool11 47 14 1 59 813 702 68
pool12 430 22 10 7793 15494 6124 724
pool13 344 3 1 98 7080 5443 384
pool14 2513 1 13 246 5311 3815 208
pool15 252 0 5 561 7890 4618 241
pool16 1570 1 14 351 7400 6714 309
pool17 439 0 2 24 5888 5314 444
pool18 611 1 3 525 6870 4912 409
pool19 716 1727 7 637 9902 8359 646
pool2 257 7 3 1044 2768 6087 334
pool20 366 1 6 183 2713 2617 278
pool21 7542 8 9 489 6753 8498 1122
pool22 427 2 3 277 5266 7121 437
pool23 326 0 4 45 7324 5902 309
pool24 105 0 2 238 9577 6335 583
pool3 171 6 11 1799 3835 5104 216
pool4 308 0 7 406 4411 7302 268
pool5 232 1 0 1918 6940 5429 187
pool6 3219 0 7 471 5741 8541 376
pool7 244 92 6 608 5545 3716 158
pool8 193 0 4 621 5181 4128 127
pool9 401 0 1 50 6098 5631 591
PoolM 20993 93 13 4164 6773 441 3063
PoolMM 14788 171 8 272 12343 338 2003
Undetermined 472 121 144 4070 11482 7192 810
yy <- t(y/rowSums(y) * 100)

par(mar=c(5, 10, 5, 2))
barplot(yy,horiz=TRUE,las=1,cex.names=0.6,xlab="proportion of reads (%)",
  legend.text=TRUE,col=brewer.pal(n = 7, name = "Set1"),
  args.legend = list(x = "left" , bty = "n", inset=c(-0.3, -0.15), cex=0.8))
grid()

yy <- yy[,which( ! colnames(yy) %in% c("Neg","101-1023","185-1135","7185","NTC","Pool1")   )]

colfunc <- colorRampPalette(c("white", "blue"))

heatmap.2(yy,trace="none",scale="none",col=colfunc(25))

Look at on-target reads

Here we have a summary of the reads that were on target for each amplicon for each individual.

myfiles <- list.files("fastq/",pattern="bedgraph.intersect",full.names=TRUE)

ont <- lapply(myfiles, function(x)  { y <- read.table(x,header=TRUE) ; y  }  )

names(ont) <- gsub(".bam.bedgraph.intersect","",gsub("fastq//","",myfiles))

ont
## $`101-1023`
## [1] chr     start   end     n_reads chr.1   start.1 end.1   gene    overlap
## <0 rows> (or 0-length row.names)
## 
## $`185-1135`
## [1] chr     start   end     n_reads chr.1   start.1 end.1   gene    overlap
## <0 rows> (or 0-length row.names)
## 
## $`7185`
## [1] chr     start   end     n_reads chr.1   start.1 end.1   gene    overlap
## <0 rows> (or 0-length row.names)
## 
## $Neg
## [1] chr     start   end     n_reads chr.1   start.1 end.1   gene    overlap
## <0 rows> (or 0-length row.names)
## 
## $NTC
## [1] chr     start   end     n_reads chr.1   start.1 end.1   gene    overlap
## <0 rows> (or 0-length row.names)
## 
## $pool1
##    chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1   17  78358468  78358619    3926    17  78358469  78358619  SOCS3     150
## 2    2  25161598  25161834    8075     2  25161598  25161833 POMC_2     235
## 3    2  25168372  25168396    8405     2  25168373  25168611 POMC_1      23
## 4    2  25168587  25168608    8389     2  25168373  25168611 POMC_1      21
## 5    6  31575209  31575467    1673     6  31575210  31575467    TNF     257
## 6    7  24283795  24283937    8358     7  24283548  24283843  NPY_1      48
## 7    7  24283795  24283937    8358     7  24283796  24283936  NPY_2     140
## 8    7 128241096 128241289     181     7 128241036 128241347    LEP     193
## 9    7 128241325 128241326     100     7 128241036 128241347    LEP       1
## 10   7 128241327 128241330     100     7 128241036 128241347    LEP       3
## 11   7 128241331 128241347     100     7 128241036 128241347    LEP      16
## 
## $pool10
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    4990    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    4764     2  25161598  25161833 POMC_2     235
## 3   2  25168588  25168608     163     2  25168373  25168611 POMC_1      20
## 4   6  31575209  31575467     800     6  31575210  31575467    TNF     257
## 5   7  24283596  24283937    5412     7  24283548  24283843  NPY_1     247
## 6   7  24283596  24283937    5412     7  24283796  24283936  NPY_2     140
## 7   7 128241038 128241347     946     7 128241036 128241347    LEP     309
## 
## $pool11
##   chr    start      end n_reads chr.1  start.1    end.1   gene overlap
## 1  17 78358468 78358619     702    17 78358469 78358619  SOCS3     150
## 2   2 25161598 25161833     565     2 25161598 25161833 POMC_2     235
## 3   7 24283795 24283936     789     7 24283548 24283843  NPY_1      48
## 4   7 24283795 24283936     789     7 24283796 24283936  NPY_2     140
## 
## $pool12
##    chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1   17  78358468  78358619    6121    17  78358469  78358619  SOCS3     150
## 2    2  25161598  25161834    8456     2  25161598  25161833 POMC_2     235
## 3    2  25168372  25168395    3898     2  25168373  25168611 POMC_1      22
## 4    2  25168587  25168608    3894     2  25168373  25168611 POMC_1      21
## 5    6  31575209  31575467     680     6  31575210  31575467    TNF     257
## 6    7  24283547  24283571     105     7  24283548  24283843  NPY_1      23
## 7    7  24283572  24283574     105     7  24283548  24283843  NPY_1       2
## 8    7  24283594  24283937    7371     7  24283548  24283843  NPY_1     249
## 9    7  24283594  24283937    7371     7  24283796  24283936  NPY_2     140
## 10   7 128241038 128241347     425     7 128241036 128241347    LEP     309
## 
## $pool13
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    5441    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    5070     2  25161598  25161833 POMC_2     235
## 3   6  31575209  31575467     378     6  31575210  31575467    TNF     257
## 4   7  24283795  24283937    6543     7  24283548  24283843  NPY_1      48
## 5   7  24283795  24283937    6543     7  24283796  24283936  NPY_2     140
## 6   7 128241038 128241347     343     7 128241036 128241347    LEP     309
## 
## $pool14
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    3815    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    3527     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     123     2  25168373  25168611 POMC_1      22
## 4   2  25168588  25168608     123     2  25168373  25168611 POMC_1      20
## 5   6  31575209  31575467     197     6  31575210  31575467    TNF     257
## 6   7  24283795  24283937    6127     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937    6127     7  24283796  24283936  NPY_2     140
## 8   7 128241095 128241289     189     7 128241036 128241347    LEP     194
## 9   7 128241308 128241347    2418     7 128241036 128241347    LEP      39
## 
## $pool15
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    4617    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    5093     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     283     2  25168373  25168611 POMC_1      22
## 4   2  25168588  25168608     278     2  25168373  25168611 POMC_1      20
## 5   6  31575209  31575467     241     6  31575210  31575467    TNF     257
## 6   7  24283795  24283937    5637     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937    5637     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347     238     7 128241036 128241347    LEP     309
## 
## $pool16
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    6713    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    6234     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168399     194     2  25168373  25168611 POMC_1      26
## 4   2  25168587  25168608     191     2  25168373  25168611 POMC_1      21
## 5   6  31575209  31575467     305     6  31575210  31575467    TNF     257
## 6   7  24283547  24283937    8142     7  24283548  24283843  NPY_1     295
## 7   7  24283547  24283937    8142     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347    1342     7 128241036 128241347    LEP     309
## 
## $pool17
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    5312    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    5144     2  25161598  25161833 POMC_2     235
## 3   6  31575209  31575467     443     6  31575210  31575467    TNF     257
## 4   7  24283547  24283937    5562     7  24283548  24283843  NPY_1     295
## 5   7  24283547  24283937    5562     7  24283796  24283936  NPY_2     140
## 6   7 128241038 128241347     437     7 128241036 128241347    LEP     309
## 
## $pool18
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    4911    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    5568     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     266     2  25168373  25168611 POMC_1      22
## 4   2  25168588  25168608     258     2  25168373  25168611 POMC_1      20
## 5   6  31575209  31575467     407     6  31575210  31575467    TNF     257
## 6   7  24283596  24283937    6002     7  24283548  24283843  NPY_1     247
## 7   7  24283596  24283937    6002     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347     609     7 128241036 128241347    LEP     309
## 
## $pool19
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    8358    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    7748     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     320     2  25168373  25168611 POMC_1      22
## 4   2  25168587  25168608     317     2  25168373  25168611 POMC_1      21
## 5   6  31575209  31575467     641     6  31575210  31575467    TNF     257
## 6   7  24283547  24283579    1798     7  24283548  24283843  NPY_1      31
## 7   7  24283594  24283937    8417     7  24283548  24283843  NPY_1     249
## 8   7  24283594  24283937    8417     7  24283796  24283936  NPY_2     140
## 9   7 128241038 128241347     712     7 128241036 128241347    LEP     309
## 
## $pool2
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    6087    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    2676     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168397     523     2  25168373  25168611 POMC_1      24
## 4   2  25168587  25168608     520     2  25168373  25168611 POMC_1      21
## 5   6  31575209  31575467     313     6  31575210  31575467    TNF     257
## 6   7  24283795  24283937    8780     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937    8780     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347     250     7 128241036 128241347    LEP     309
## 
## $pool20
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    2617    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    2434     2  25161598  25161833 POMC_2     235
## 3   6  31575209  31575467     260     6  31575210  31575467    TNF     257
## 4   7  24283795  24283937    3641     7  24283548  24283843  NPY_1      48
## 5   7  24283795  24283937    3641     7  24283796  24283936  NPY_2     140
## 6   7 128241038 128241347     364     7 128241036 128241347    LEP     309
## 
## $pool21
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    8496    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    6397     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168399     353     2  25168373  25168611 POMC_1      26
## 4   2  25168587  25168608     135     2  25168373  25168611 POMC_1      21
## 5   6  31575209  31575467    1058     6  31575210  31575467    TNF     257
## 6   7  24283594  24283937   10087     7  24283548  24283843  NPY_1     249
## 7   7  24283594  24283937   10087     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347    7369     7 128241036 128241347    LEP     309
## 
## $pool22
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    7121    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    5127     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     139     2  25168373  25168611 POMC_1      22
## 4   2  25168588  25168608     138     2  25168373  25168611 POMC_1      20
## 5   6  31575209  31575467     401     6  31575210  31575467    TNF     257
## 6   7  24283795  24283937    9874     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937    9874     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347     417     7 128241036 128241347    LEP     309
## 
## $pool23
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    5898    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161836    5988     2  25161598  25161833 POMC_2     235
## 3   6  31575209  31575467     305     6  31575210  31575467    TNF     257
## 4   7  24283795  24283937    8303     7  24283548  24283843  NPY_1      48
## 5   7  24283795  24283937    8303     7  24283796  24283936  NPY_2     140
## 6   7 128241038 128241347     325     7 128241036 128241347    LEP     309
## 
## $pool24
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    6334    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    7554     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     121     2  25168373  25168611 POMC_1      22
## 4   2  25168587  25168608     117     2  25168373  25168611 POMC_1      21
## 5   6  31575209  31575467     581     6  31575210  31575467    TNF     257
## 6   7  24283547  24283937    6642     7  24283548  24283843  NPY_1     295
## 7   7  24283547  24283937    6642     7  24283796  24283936  NPY_2     140
## 8   7 128241100 128241250     102     7 128241036 128241347    LEP     150
## 9   7 128241251 128241287     102     7 128241036 128241347    LEP      36
## 
## $pool3
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    5104    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    2930     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     900     2  25168373  25168611 POMC_1      22
## 4   2  25168587  25168608     896     2  25168373  25168611 POMC_1      21
## 5   6  31575209  31575467     209     6  31575210  31575467    TNF     257
## 6   7  24283795  24283937    6628     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937    6628     7  24283796  24283936  NPY_2     140
## 8   7 128241096 128241289     162     7 128241036 128241347    LEP     193
## 
## $pool4
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    7301    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    3965     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168399     205     2  25168373  25168611 POMC_1      26
## 4   2  25168587  25168608     201     2  25168373  25168611 POMC_1      21
## 5   6  31575209  31575467     265     6  31575210  31575467    TNF     257
## 6   7  24283795  24283937    9276     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937    9276     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347     303     7 128241036 128241347    LEP     309
## 
## $pool5
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    5429    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    4689     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168399     960     2  25168373  25168611 POMC_1      26
## 4   2  25168587  25168608     959     2  25168373  25168611 POMC_1      21
## 5   6  31575216  31575460     185     6  31575210  31575467    TNF     244
## 6   7  24283795  24283937    8064     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937    8064     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347     226     7 128241036 128241347    LEP     309
## 
## $pool6
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    8539    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    4964     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168395     239     2  25168373  25168611 POMC_1      22
## 4   2  25168588  25168608     232     2  25168373  25168611 POMC_1      20
## 5   6  31575209  31575467     375     6  31575210  31575467    TNF     257
## 6   7  24283795  24283937   11321     7  24283548  24283843  NPY_1      48
## 7   7  24283795  24283937   11321     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347    3042     7 128241036 128241347    LEP     309
## 
## $pool7
##    chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1   17  78358468  78358619    3716    17  78358469  78358619  SOCS3     150
## 2    2  25161598  25161834    3472     2  25161598  25161833 POMC_2     235
## 3    2  25168372  25168395     307     2  25168373  25168611 POMC_1      22
## 4    2  25168588  25168608     303     2  25168373  25168611 POMC_1      20
## 5    6  31575216  31575460     158     6  31575210  31575467    TNF     244
## 6    7  24283547  24283573     107     7  24283548  24283843  NPY_1      25
## 7    7  24283795  24283937    5981     7  24283548  24283843  NPY_1      48
## 8    7  24283795  24283937    5981     7  24283796  24283936  NPY_2     140
## 9    7 128241096 128241289     175     7 128241036 128241347    LEP     193
## 10   7 128241322 128241347     155     7 128241036 128241347    LEP      25
## 
## $pool8
##    chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1   17  78358468  78358619    4125    17  78358469  78358619  SOCS3     150
## 2    2  25161598  25161834    3366     2  25161598  25161833 POMC_2     235
## 3    2  25168372  25168395     312     2  25168373  25168611 POMC_1      22
## 4    2  25168588  25168608     309     2  25168373  25168611 POMC_1      20
## 5    6  31575217  31575255     112     6  31575210  31575467    TNF      38
## 6    6  31575442  31575460     111     6  31575210  31575467    TNF      18
## 7    7  24283795  24283937    7347     7  24283548  24283843  NPY_1      48
## 8    7  24283795  24283937    7347     7  24283796  24283936  NPY_2     140
## 9    7 128241096 128241289     173     7 128241036 128241347    LEP     193
## 10   7 128241322 128241347     105     7 128241036 128241347    LEP      25
## 
## $pool9
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619    5629    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    5752     2  25161598  25161833 POMC_2     235
## 3   6  31575209  31575467     591     6  31575210  31575467    TNF     257
## 4   7  24283596  24283937    6314     7  24283548  24283843  NPY_1     247
## 5   7  24283596  24283937    6314     7  24283796  24283936  NPY_2     140
## 6   7 128241038 128241347     389     7 128241036 128241347    LEP     309
## 
## $PoolM
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619     401    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161834    6413     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168608    4055     2  25168373  25168611 POMC_1     235
## 4   6  31575209  31575467    2469     6  31575210  31575467    TNF     257
## 5   7  24283547  24283572     148     7  24283548  24283843  NPY_1      24
## 6   7  24283596  24283937    8978     7  24283548  24283843  NPY_1     247
## 7   7  24283596  24283937    8978     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347   20618     7 128241036 128241347    LEP     309
## 
## $PoolMM
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358468  78358619     330    17  78358469  78358619  SOCS3     150
## 2   2  25161598  25161620    4262     2  25161598  25161833 POMC_2      22
## 3   2  25161811  25161834    8085     2  25161598  25161833 POMC_2      22
## 4   2  25168588  25168608     185     2  25168373  25168611 POMC_1      20
## 5   6  31575209  31575467    1293     6  31575210  31575467    TNF     257
## 6   7  24283547  24283573     208     7  24283548  24283843  NPY_1      25
## 7   7  24283795  24283937    6895     7  24283548  24283843  NPY_1      48
## 8   7  24283795  24283937    6895     7  24283796  24283936  NPY_2     140
## 9   7 128241038 128241347   14608     7 128241036 128241347    LEP     309
## 
## $Undetermined
##   chr     start       end n_reads chr.1   start.1     end.1   gene overlap
## 1  17  78358465  78358621    7129    17  78358469  78358619  SOCS3     150
## 2   2  25161596  25161836    8205     2  25161598  25161833 POMC_2     235
## 3   2  25168372  25168608    2184     2  25168373  25168611 POMC_1     235
## 4   6  31575209  31575467     580     6  31575210  31575467    TNF     257
## 5   7  24283547  24283578     174     7  24283548  24283843  NPY_1      30
## 6   7  24283594  24283937   10388     7  24283548  24283843  NPY_1     249
## 7   7  24283594  24283937   10388     7  24283796  24283936  NPY_2     140
## 8   7 128241038 128241347     371     7 128241036 128241347    LEP     309

Look at off-target reads

Here we have the details of each of the off-target genomic regions that were identified in this assay. I’ve also got the location of the closest gene.

myfiles <- list.files("fastq/",pattern=".bedgraph.offtarget.genes$",full.names=TRUE)

oft <- lapply(myfiles, function(x)  { y <- read.table(x,header=TRUE) ; y  }  )

names(oft) <- gsub(".bam.bedgraph.offtarget.genes","",gsub("fastq//","",myfiles))

oft
## $`101-1023`
##   chr    start      end n_reads chr.1  start.1    end.1  gene dist_bp
## 1  19 35358874 35358981   27777    19 35358460 35360489 FFAR3       0
## 2  19 35371343 35371444   27968    19 35370929 35372962 GPR42       0
## 
## $`185-1135`
##   chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1  19  35358949  35359135   24019    19  35358460  35360489      FFAR3       0
## 2  19  35371418  35371604   24643    19  35370929  35372962      GPR42       0
## 3   6 158378467 158378509     113     6 158232236 158511828      TULP4       0
## 4   6 158378467 158378509     113     6 158282841 158428379 AL360169.2       0
## 
## $`7185`
##   chr     start       end n_reads chr.1   start.1     end.1   gene dist_bp
## 1  19  35358949  35359142   20615    19  35358460  35360489  FFAR3       0
## 2  19  35371418  35371611   19032    19  35370929  35372962  GPR42       0
## 3   2 152619971 152620002     102     2 152335174 152649826  FMNL2       0
## 4   7  39369845  39369878     156     7  38977909  39493095 POU6F2       0
## 5   X 112340564 112340598     109     X 112319952 112320417 DPRXP7   20148
## 
## $Neg
## [1] chr     start   end     n_reads chr.1   start.1 end.1   gene    dist_bp
## <0 rows> (or 0-length row.names)
## 
## $NTC
## [1] chr     start   end     n_reads chr.1   start.1 end.1   gene    dist_bp
## <0 rows> (or 0-length row.names)
## 
## $pool1
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611316     259     1  18595414  18595636 AL031737.1   15620
## 2    1 162034657 162034667     417     1 162039016 162039567 AL590408.1    4350
## 3    1 162034670 162034712     418     1 162039016 162039567 AL590408.1    4305
## 4   10   6307526   6307583     195    10   6271169   6353827  LINC02649       0
## 5   11  65786127  65786205     111    11  65787063  65797214      OVOL1     859
## 6   17   4550782   4550844     593    17   4538897   4555386    MYBBP1A       0
## 7   19  13908861  13908908     118    19  13906201  13930879     CC2D1A       0
## 8    2  35765764  35765776     145     2  35724759  35725142   MRPL50P1   40623
## 9    2  35765778  35765802     146     2  35724759  35725142   MRPL50P1   40637
## 10   2  35765803  35765822     146     2  35724759  35725142   MRPL50P1   40662
## 11  22  46679451  46679485     216    22  46576012  46679790     GRAMD4       0
## 12   3  60181850  60181902    4490     3  59747277  61251459       FHIT       0
## 13   3 186110029 186110063     153     3 186046314 186110318       ETV5       0
## 14   3 186110029 186110063     153     3 186105668 186362234       DGKG       0
## 15   3 186110064 186110092     153     3 186046314 186110318       ETV5       0
## 16   3 186110064 186110092     153     3 186105668 186362234       DGKG       0
## 17   4   8288864   8288951    2355     4   8269754   8307098      HTRA3       0
## 18   5    865245    865502     767     5    850291    892801       BRD9       0
## 19   5  10649438  10649513   15302     5  10564070  10657816   ANKRD33B       0
## 20   5 119023122 119023140    4411     5 119006347 119070902 AC008629.1       0
## 21   5 119023143 119023175    4421     5 119006347 119070902 AC008629.1       0
## 22   5 131945721 131945786     896     5 131807143 132011637 AC034228.3       0
## 23   5 131945721 131945786     896     5 131944408 131968220 AC034228.2       0
## 24   5 131945789 131945799     887     5 131807143 132011637 AC034228.3       0
## 25   5 131945789 131945799     887     5 131944408 131968220 AC034228.2       0
## 26   8  22055623  22055743    4150     8  22048995  22082527       DMTN       0
## 27   8  39240838  39240870     693     8  39106990  39284917     ADAM32       0
## 28   X  13044583  13044596     167     X  13035617  13044682      FAM9C       0
## 29   X  13044599  13044672     174     X  13035617  13044682      FAM9C       0
## 30   Y  12869918  12869975     222     Y  12537650  12860839      USP9Y    9080
## 
## $pool10
##    chr     start       end n_reads chr.1   start.1     end.1        gene
## 1    1 234742415 234742439     763     1 234724042 234736720   LINC01132
## 2   10  10027960  10028013     239    10  10058722  10063502   LINC02670
## 3   12 105330759 105330791     224    12 105235290 105396097    C12orf75
## 4   16  14989690  14989869     168    16  14974591  15139339      PDXDC1
## 5   16  14989690  14989869     168    16  14988259  14990160  AC138932.2
## 6   18  10590130  10590154     759    18  10594590  10604798  AP001099.1
## 7   18  37891155  37891201    3213    18  37960220  37992413  AC108452.1
## 8   19   1600354   1600378     708    19   1578339   1605445  AC005943.1
## 9   19   1600354   1600378     708    19   1597169   1605473      UQCR11
## 10  19  38326060  38326071     139    19  38319845  38332076       KCNK6
## 11  19  38326072  38326126     140    19  38319845  38332076       KCNK6
## 12  19  46791472  46791496     228    19  46787815  46789043  AC008622.2
## 13  19  48855456  48855480     706    19  48837097  48868617     PLEKHA4
## 14   2 119593691 119593715     682     2 119544432 119662251     CFAP221
## 15  22  46679451  46679485     211    22  46576012  46679790      GRAMD4
## 16   4   8288864   8288951    3647     4   8269754   8307098       HTRA3
## 17   4  78422580  78422696     168     4  78057323  78544269       FRAS1
## 18   4  78422698  78422709     163     4  78057323  78544269       FRAS1
## 19   5    865245    865502    1648     5    850291    892801        BRD9
## 20   5  10649438  10649513    6749     5  10564070  10657816    ANKRD33B
## 21   5 131945721 131945786    1352     5 131807143 132011637  AC034228.3
## 22   5 131945721 131945786    1352     5 131944408 131968220  AC034228.2
## 23   5 131945788 131945799    1328     5 131807143 132011637  AC034228.3
## 24   5 131945788 131945799    1328     5 131944408 131968220  AC034228.2
## 25   7  86652471  86652495     233     7  86643914  86864884        GRM3
## 26   8   1974504   1974546    2771     8   1971153   1974637  AC019257.1
## 27   8   1974504   1974546    2771     8   1971397   1976478 KBTBD11-OT1
## 28   8   1974504   1974546    2771     8   1973677   2006936     KBTBD11
## 29   8  22055623  22055743    3445     8  22048995  22082527        DMTN
##    dist_bp
## 1     5696
## 2    30710
## 3        0
## 4        0
## 5        0
## 6     4437
## 7    69020
## 8        0
## 9        0
## 10       0
## 11       0
## 12    2430
## 13       0
## 14       0
## 15       0
## 16       0
## 17       0
## 18       0
## 19       0
## 20       0
## 21       0
## 22       0
## 23       0
## 24       0
## 25       0
## 26       0
## 27       0
## 28       0
## 29       0
## 
## $pool11
##   chr    start      end n_reads chr.1  start.1    end.1     gene dist_bp
## 1   4  8288864  8288951     403     4  8269754  8307098    HTRA3       0
## 2   5   865245   865490     213     5   850291   892801     BRD9       0
## 3   5   865491   865502     113     5   850291   892801     BRD9       0
## 4   5 10649439 10649513     955     5 10564070 10657816 ANKRD33B       0
## 5   8 22055623 22055726     402     8 22048995 22082527     DMTN       0
## 6   8 22055727 22055743     401     8 22048995 22082527     DMTN       0
## 
## $pool12
##    chr     start       end n_reads chr.1   start.1     end.1        gene
## 1    1  18611255  18611340    1032     1  18595414  18595636  AL031737.1
## 2    1  58306257  58306325     156     1  56994778  58546734        DAB1
## 3    1 241065370 241065403     653     1 240775514 241357230        RGS7
## 4   10   6307518   6307583     670    10   6271169   6353827   LINC02649
## 5   10  70183632  70183662     141    10  70147289  70170523       SAR1A
## 6   10  83229789  83229800     316    10  83311628  83314475    MARK2P15
## 7   10  83229801  83229848     363    10  83311628  83314475    MARK2P15
## 8   10 100122122 100122149     289    10 100105754 100140151    CYP2C23P
## 9   10 100122170 100122193     284    10 100105754 100140151    CYP2C23P
## 10  11  25874404  25874455     106    11  25924188  25926808  AC013799.1
## 11  11  65726854  65726937     348    11  65726939  65728214     KRT8P26
## 12  15  20074892  20074922     223    15  20073699  20074334     BCAR1P1
## 13  15  21082005  21082035     183    15  21080812  21081447     BCAR1P2
## 14  16  14989693  14989868     116    16  14974591  15139339      PDXDC1
## 15  16  14989693  14989868     116    16  14988259  14990160  AC138932.2
## 16  16  17690789  17690800     208    16  17825252  17826906  AC025277.1
## 17  16  17690802  17690847     210    16  17825252  17826906  AC025277.1
## 18  16  18089070  18089116     109    16  17933189  18151595  AC010601.1
## 19  16  18089070  18089116     109    16  18002806  18173063  AC091489.1
## 20  17   4550782   4550844     206    17   4538897   4555386     MYBBP1A
## 21   2  95526518  95526601     268     2  95525109  95526702 AC009237.14
## 22   2  95526518  95526601     268     2  95525345  95532405  AC009237.3
## 23  22  46679451  46679485     252    22  46576012  46679790      GRAMD4
## 24   3 196196004 196196051     123     3 196197452 196211437     ZDHHC19
## 25   4   8288864   8288951     608     4   8269754   8307098       HTRA3
## 26   5    865245    865502    1154     5    850291    892801        BRD9
## 27   5  10649438  10649513   11895     5  10564070  10657816    ANKRD33B
## 28   5 131945721 131945786     875     5 131807143 132011637  AC034228.3
## 29   5 131945721 131945786     875     5 131944408 131968220  AC034228.2
## 30   5 131945789 131945799     862     5 131807143 132011637  AC034228.3
## 31   5 131945789 131945799     862     5 131944408 131968220  AC034228.2
## 32   5 181195621 181195635     113     5 181193924 181205293       TRIM7
## 33   5 181195621 181195635     113     5 181195496 181203103   TRIM7-AS1
## 34   5 181195639 181195726     116     5 181193924 181205293       TRIM7
## 35   5 181195639 181195726     116     5 181195496 181203103   TRIM7-AS1
## 36   5 181195730 181195744     103     5 181193924 181205293       TRIM7
## 37   5 181195730 181195744     103     5 181195496 181203103   TRIM7-AS1
## 38   6  30466891  30466928     554     6  30466452  30467994      TMPOP1
## 39   6  62467363  62467402     481     6  62460940  62461503      DHFRP5
## 40   6  62467511  62467538     481     6  62460940  62461503      DHFRP5
## 41   8  22055623  22055743    4658     8  22048995  22082527        DMTN
## 42   8  37701095  37701196     243     8  37695782  37700019      ZNF703
## 43   X  54367258  54367275     718     X  54192823  54358642        WNK3
## 44   X  54367276  54367320     740     X  54192823  54358642        WNK3
## 45   Y  12869910  12869975     675     Y  12537650  12860839       USP9Y
##    dist_bp
## 1    15620
## 2        0
## 3        0
## 4        0
## 5    13110
## 6    81829
## 7    81781
## 8        0
## 9        0
## 10   49734
## 11       3
## 12     559
## 13     559
## 14       0
## 15       0
## 16  134453
## 17  134406
## 18       0
## 19       0
## 20       0
## 21       0
## 22       0
## 23       0
## 24    1402
## 25       0
## 26       0
## 27       0
## 28       0
## 29       0
## 30       0
## 31       0
## 32       0
## 33       0
## 34       0
## 35       0
## 36       0
## 37       0
## 38       0
## 39    5861
## 40    6009
## 41       0
## 42    1077
## 43    8617
## 44    8635
## 45    9072
## 
## $pool13
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611324     187     1  18595414  18595636 AL031737.1   15620
## 2   10   6307518   6307583     183    10   6271169   6353827  LINC02649       0
## 3   10 132135162 132135199     121    10 132036336 132184858    JAKMIP3       0
## 4    2 221871203 221871265    1343     2 221944223 221944612     LLPHP3   72959
## 5   22  46679451  46679485     181    22  46576012  46679790     GRAMD4       0
## 6    4   8288864   8288951    2343     4   8269754   8307098      HTRA3       0
## 7    5    865245    865502    1563     5    850291    892801       BRD9       0
## 8    5  10649438  10649513    9952     5  10564070  10657816   ANKRD33B       0
## 9    5 131945721 131945786     637     5 131807143 132011637 AC034228.3       0
## 10   5 131945721 131945786     637     5 131944408 131968220 AC034228.2       0
## 11   5 131945789 131945799     624     5 131807143 132011637 AC034228.3       0
## 12   5 131945789 131945799     624     5 131944408 131968220 AC034228.2       0
## 13   7  37256513  37256545     105     7  36852906  37449223      ELMO1       0
## 14   7  37256766  37256788     105     7  36852906  37449223      ELMO1       0
## 15   8  22055623  22055743    2591     8  22048995  22082527       DMTN       0
## 16   9  93435058  93435107     109     9  93431441  93453581  FAM120AOS       0
## 17   X  82446629  82446671    4642     X  82497669  82497924    EIF3JP1   50999
## 18   X  82446673  82446687    4579     X  82497669  82497924    EIF3JP1   50983
## 19   Y  12869910  12869975     184     Y  12537650  12860839      USP9Y    9072
## 
## $pool14
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611324     268     1  18595414  18595636 AL031737.1   15620
## 2   10   6307518   6307583     263    10   6271169   6353827  LINC02649       0
## 3   11   1181147   1181217     222    11   1157953   1201138     MUC5AC       0
## 4   16  14989690  14989868     107    16  14974591  15139339     PDXDC1       0
## 5   16  14989690  14989868     107    16  14988259  14990160 AC138932.2       0
## 6   16  48441125  48441181     130    16  48356364  48448402      SIAH1       0
## 7   17  43755387  43755414     154    17  43753738  43758791       SOST       0
## 8   17  43755415  43755424     154    17  43753738  43758791       SOST       0
## 9    2 234950963 234951013     112     2 234952017 235055714     SH3BP4    1005
## 10  20  36986623  36986655     824    20  36996349  37095997       RBL1    9695
## 11  22  46679451  46679485     776    22  46576012  46679790     GRAMD4       0
## 12   4   8288864   8288959    1995     4   8269754   8307098      HTRA3       0
## 13   5    865245    865502     793     5    850291    892801       BRD9       0
## 14   5  10649438  10649513   10509     5  10564070  10657816   ANKRD33B       0
## 15   5 131945721 131945799    1567     5 131807143 132011637 AC034228.3       0
## 16   5 131945721 131945799    1567     5 131944408 131968220 AC034228.2       0
## 17   8  22055623  22055743    4470     8  22048995  22082527       DMTN       0
## 18   Y  12869910  12869975     278     Y  12537650  12860839      USP9Y    9072
## 
## $pool15
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611336     621     1  18595414  18595636 AL031737.1   15620
## 2   10   6307508   6307583     570    10   6271169   6353827  LINC02649       0
## 3   10  70183632  70183662     106    10  70147289  70170523      SAR1A   13110
## 4   10 100122122 100122149     144    10 100105754 100140151   CYP2C23P       0
## 5   10 100122170 100122193     140    10 100105754 100140151   CYP2C23P       0
## 6   22  46679451  46679485     815    22  46576012  46679790     GRAMD4       0
## 7    4   8288864   8288951     309     4   8269754   8307098      HTRA3       0
## 8    5    865245    865502     938     5    850291    892801       BRD9       0
## 9    5  10649438  10649513   11662     5  10564070  10657816   ANKRD33B       0
## 10   5 131945721 131945786    1053     5 131807143 132011637 AC034228.3       0
## 11   5 131945721 131945786    1053     5 131944408 131968220 AC034228.2       0
## 12   5 131945789 131945799    1043     5 131807143 132011637 AC034228.3       0
## 13   5 131945789 131945799    1043     5 131944408 131968220 AC034228.2       0
## 14   6  62467363  62467402     155     6  62460940  62461503     DHFRP5    5861
## 15   6  62467511  62467538     155     6  62460940  62461503     DHFRP5    6009
## 16   8  22055623  22055743    4016     8  22048995  22082527       DMTN       0
## 17   X 153867168 153867235     102     X 153861514 153886173      L1CAM       0
## 18   Y  12869910  12869975     411     Y  12537650  12860839      USP9Y    9072
## 
## $pool16
##    chr     start       end n_reads chr.1   start.1     end.1        gene
## 1    1  11748568  11748616     556     1  11736084  11754802      AGTRAP
## 2    1  18611255  18611336     726     1  18595414  18595636  AL031737.1
## 3   10   6307508   6307583     421    10   6271169   6353827   LINC02649
## 4   11   1289723   1289777     189    11   1274371   1309654      TOLLIP
## 5   16  14989690  14989869     180    16  14974591  15139339      PDXDC1
## 6   16  14989690  14989869     180    16  14988259  14990160  AC138932.2
## 7   17   4550782   4550844     300    17   4538897   4555386     MYBBP1A
## 8   22  46679451  46679485     576    22  46576012  46679790      GRAMD4
## 9    4   8288864   8288951    3404     4   8269754   8307098       HTRA3
## 10   5    865245    865502    2419     5    850291    892801        BRD9
## 11   5  10649438  10649513    9805     5  10564070  10657816    ANKRD33B
## 12   5 131945721 131945799    1392     5 131807143 132011637  AC034228.3
## 13   5 131945721 131945799    1392     5 131944408 131968220  AC034228.2
## 14   8   1974504   1974546     708     8   1971153   1974637  AC019257.1
## 15   8   1974504   1974546     708     8   1971397   1976478 KBTBD11-OT1
## 16   8   1974504   1974546     708     8   1973677   2006936     KBTBD11
## 17   8  22055623  22055743    3942     8  22048995  22082527        DMTN
## 18   8  41063496  41063528     217     8  41032892  41032998   RNU6-356P
## 19   X   2213846   2213880     141     X   2219506   2502805       DHRSX
## 20   X   2214118   2214156     144     X   2219506   2502805       DHRSX
## 21   X   3983551   3983596     328     X   3953056   3953561     RPL24P9
## 22   Y  12869918  12869975     319     Y  12537650  12860839       USP9Y
##    dist_bp
## 1        0
## 2    15620
## 3        0
## 4        0
## 5        0
## 6        0
## 7        0
## 8        0
## 9        0
## 10       0
## 11       0
## 12       0
## 13       0
## 14       0
## 15       0
## 16       0
## 17       0
## 18   30499
## 19    5627
## 20    5351
## 21   29991
## 22    9080
## 
## $pool17
##   chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1   4   8288864   8288951    3435     4   8269754   8307098      HTRA3       0
## 2   5    865252    865490     133     5    850291    892801       BRD9       0
## 3   5  10649438  10649513   12054     5  10564070  10657816   ANKRD33B       0
## 4   5 131945721 131945786     510     5 131807143 132011637 AC034228.3       0
## 5   5 131945721 131945786     510     5 131944408 131968220 AC034228.2       0
## 6   5 131945789 131945799     504     5 131807143 132011637 AC034228.3       0
## 7   5 131945789 131945799     504     5 131944408 131968220 AC034228.2       0
## 8   8  22055623  22055743    1924     8  22048995  22082527       DMTN       0
## 
## $pool18
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611336     335     1  18595414  18595636 AL031737.1   15620
## 2   10   6307522   6307583     121    10   6271169   6353827  LINC02649       0
## 3   10 131347243 131347276     103    10 131092391 131311721    TCERG1L   35523
## 4   16  14989617  14989628     150    16  14974591  15139339     PDXDC1       0
## 5   16  14989617  14989628     150    16  14988259  14990160 AC138932.2       0
## 6   16  14989629  14989930     302    16  14974591  15139339     PDXDC1       0
## 7   16  14989629  14989930     302    16  14988259  14990160 AC138932.2       0
## 8   22  29788944  29789092     197    22  29788609  29838304      ASCC2       0
## 9   22  29789093  29789115     197    22  29788609  29838304      ASCC2       0
## 10  22  29789117  29789132     196    22  29788609  29838304      ASCC2       0
## 11  22  46679451  46679485     185    22  46576012  46679790     GRAMD4       0
## 12   4   8288864   8288951    1958     4   8269754   8307098      HTRA3       0
## 13   4  31367013  31367064     316     4  31350284  31351725 AC104071.1   15289
## 14   5    865245    865502    2675     5    850291    892801       BRD9       0
## 15   5  10649438  10649513    6016     5  10564070  10657816   ANKRD33B       0
## 16   5 131945721 131945786     536     5 131807143 132011637 AC034228.3       0
## 17   5 131945721 131945786     536     5 131944408 131968220 AC034228.2       0
## 18   5 131945789 131945799     526     5 131807143 132011637 AC034228.3       0
## 19   5 131945789 131945799     526     5 131944408 131968220 AC034228.2       0
## 20   8  22055623  22055743    2302     8  22048995  22082527       DMTN       0
## 21   Y  12869910  12869975     127     Y  12537650  12860839      USP9Y    9072
## 
## $pool19
##    chr     start       end n_reads chr.1   start.1     end.1        gene
## 1   11 115173455 115173532     313    11 115169218 115504957       CADM1
## 2   12 132583203 132583212     344    12 132489551 132585188      FBRSL1
## 3   12 132583214 132583258     345    12 132489551 132585188      FBRSL1
## 4   13  69077731  69077797     210    13  69101832  69102056     SNRPFP3
## 5   16  14989689  14989870     197    16  14974591  15139339      PDXDC1
## 6   16  14989689  14989870     197    16  14988259  14990160  AC138932.2
## 7   16  66767740  66767838     201    16  66754640  66801620       TERB1
## 8   17   4550782   4550844     138    17   4538897   4555386     MYBBP1A
## 9    2  95526518  95526601     111     2  95525109  95526702 AC009237.14
## 10   2  95526518  95526601     111     2  95525345  95532405  AC009237.3
## 11  22  46679451  46679485     443    22  46576012  46679790      GRAMD4
## 12   4   8288864   8288955    4024     4   8269754   8307098       HTRA3
## 13   5    865245    865502    3139     5    850291    892801        BRD9
## 14   5  10649438  10649513   11258     5  10564070  10657816    ANKRD33B
## 15   5 131945721 131945786    1376     5 131807143 132011637  AC034228.3
## 16   5 131945721 131945786    1376     5 131944408 131968220  AC034228.2
## 17   5 131945789 131945799    1358     5 131807143 132011637  AC034228.3
## 18   5 131945789 131945799    1358     5 131944408 131968220  AC034228.2
## 19   8  22055623  22055743    4129     8  22048995  22082527        DMTN
##    dist_bp
## 1        0
## 2        0
## 3        0
## 4    24036
## 5        0
## 6        0
## 7        0
## 8        0
## 9        0
## 10       0
## 11       0
## 12       0
## 13       0
## 14       0
## 15       0
## 16       0
## 17       0
## 18       0
## 19       0
## 
## $pool2
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611336     555     1  18595414  18595636 AL031737.1   15620
## 2   10   6307518   6307583     399    10   6271169   6353827  LINC02649       0
## 3   10 100122122 100122193     203    10 100105754 100140151   CYP2C23P       0
## 4   12   7913634   7913754     229    12   7919230   7936187     SLC2A3    5477
## 5   17  81103010  81103061     310    17  81035122  81117432     BAIAP2       0
## 6   17  81103064  81103080     298    17  81035122  81117432     BAIAP2       0
## 7   22  46679451  46679485     818    22  46576012  46679790     GRAMD4       0
## 8    3  14555195  14555262     136     3  14489107  14556075      GRIP2       0
## 9    4   8288864   8288951     418     4   8269754   8307098      HTRA3       0
## 10   5    865245    865502    1057     5    850291    892801       BRD9       0
## 11   5  10649438  10649513   12873     5  10564070  10657816   ANKRD33B       0
## 12   5 131945721 131945799    2815     5 131807143 132011637 AC034228.3       0
## 13   5 131945721 131945799    2815     5 131944408 131968220 AC034228.2       0
## 14   6  96925095  96925147     121     6  96924620  97140754     KLHL32       0
## 15   8  22055623  22055743    4618     8  22048995  22082527       DMTN       0
## 16   9 129284217 129284230     523     9 129282458 129312665 AL161785.1       0
## 17   9 129284232 129284318     533     9 129282458 129312665 AL161785.1       0
## 18   X  32216848  32216897     595     X  31097677  33339609        DMD       0
## 19   Y  12869905  12869975     508     Y  12537650  12860839      USP9Y    9067
## 
## $pool20
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1   10  10027960  10028013    1258    10  10058722  10063502  LINC02670   30710
## 2   16  14989617  14989628     110    16  14974591  15139339     PDXDC1       0
## 3   16  14989617  14989628     110    16  14988259  14990160 AC138932.2       0
## 4   16  14989629  14989930     224    16  14974591  15139339     PDXDC1       0
## 5   16  14989629  14989930     224    16  14988259  14990160 AC138932.2       0
## 6   21  39108618  39108702     123    21  39127568  39128040  RPL23AP12   18867
## 7   22  46679451  46679485     229    22  46576012  46679790     GRAMD4       0
## 8    4   8288864   8288967    1632     4   8269754   8307098      HTRA3       0
## 9    5    865245    865502    1593     5    850291    892801       BRD9       0
## 10   5  10649438  10649513    4777     5  10564070  10657816   ANKRD33B       0
## 11   5 131945721 131945786     143     5 131807143 132011637 AC034228.3       0
## 12   5 131945721 131945786     143     5 131944408 131968220 AC034228.2       0
## 13   5 131945789 131945799     141     5 131807143 132011637 AC034228.3       0
## 14   5 131945789 131945799     141     5 131944408 131968220 AC034228.2       0
## 15   8  22055623  22055743    2318     8  22048995  22082527       DMTN       0
## 
## $pool21
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611324     356     1  18595414  18595636 AL031737.1   15620
## 2   10   6307518   6307583     400    10   6271169   6353827  LINC02649       0
## 3   10  80473306  80473343     487    10  80454166  80533124    TSPAN14       0
## 4   10 132135162 132135199     164    10 132036336 132184858    JAKMIP3       0
## 5   12 105330765 105330791     229    12 105235290 105396097   C12orf75       0
## 6   16  14989690  14989869     171    16  14974591  15139339     PDXDC1       0
## 7   16  14989690  14989869     171    16  14988259  14990160 AC138932.2       0
## 8   20  37944304  37944312     125    20  37903111  37945350     VSTM2L       0
## 9   20  37944313  37944351     128    20  37903111  37945350     VSTM2L       0
## 10  22  43974366  43974508     202    22  43955442  44010531     SAMM50       0
## 11  22  46679451  46679485     130    22  46576012  46679790     GRAMD4       0
## 12   4   8288864   8288951    3145     4   8269754   8307098      HTRA3       0
## 13   5    865245    865502    2678     5    850291    892801       BRD9       0
## 14   5  10649438  10649513   10108     5  10564070  10657816   ANKRD33B       0
## 15   5 131945721 131945800    4480     5 131807143 132011637 AC034228.3       0
## 16   5 131945721 131945800    4480     5 131944408 131968220 AC034228.2       0
## 17   5 132200546 132200578     120     5 132190147 132295315      P4HA2       0
## 18   5 132200546 132200578     120     5 132199456 132203487 AC063976.2       0
## 19   7  63398175  63398190     101     7  63393745  63422053 AC073188.2       0
## 20   7  63398175  63398190     101     7  63396341  63399250 AC073188.6       0
## 21   7  63398175  63398190     101     7  63398046  63398957  SLC25A1P2       0
## 22   7  63398191  63398273     101     7  63393745  63422053 AC073188.2       0
## 23   7  63398191  63398273     101     7  63396341  63399250 AC073188.6       0
## 24   7  63398191  63398273     101     7  63398046  63398957  SLC25A1P2       0
## 25   8  22055623  22055743    4281     8  22048995  22082527       DMTN       0
## 26   X 153420796 153420848     102     X 153418322 153426481      ZFP92       0
## 27   X 153420849 153420964     102     X 153418322 153426481      ZFP92       0
## 28   Y  12869910  12869975     354     Y  12537650  12860839      USP9Y    9072
## 
## $pool22
##           chr     start       end n_reads      chr.1   start.1     end.1
## 1           1  18611255  18611340     317          1  18595414  18595636
## 2           1 112387835 112387898     292          1 112396214 112463456
## 3           1 112387982 112388053     292          1 112396214 112463456
## 4          10   6307518   6307583     179         10   6271169   6353827
## 5          10 131346939 131346970     375         10 131092391 131311721
## 6          10 131346990 131347017     272         10 131092391 131311721
## 7          10 131347240 131347276     648         10 131092391 131311721
## 8          11 113627262 113627297     146         11 113687547 113706373
## 9          11 113627447 113627478     145         11 113687547 113706373
## 10         13  27351867  27351917     127         13  27343687  27343746
## 11         21   8205418   8205474     107         21   8197620   8227646
## 12         21   8205475   8205485     104         21   8197620   8227646
## 13         21   8249608   8249664     111         21   8249505   8249596
## 14         21   8249665   8249675     111         21   8249505   8249596
## 15         21   8388465   8388521     110         21   8380643   8454792
## 16         21   8388522   8388532     109         21   8380643   8454792
## 17         21   8432633   8432687     102         21   8380643   8454792
## 18         22  46679451  46679485     380         22  46576012  46679790
## 19          5    865245    865502    1692          5    850291    892801
## 20          5  10649438  10649513   13348          5  10564070  10657816
## 21          5 131945721 131945799    1965          5 131807143 132011637
## 22          5 131945721 131945799    1965          5 131944408 131968220
## 23          7  37256513  37256561     126          7  36852906  37449223
## 24          7  37256753  37256804     123          7  36852906  37449223
## 25          8  22055623  22055743    4642          8  22048995  22082527
## 26 GL000220.1    104835    104891     107 GL000220.1    105287    105376
## 27 GL000220.1    104892    104902     106 GL000220.1    105287    105376
## 28 KI270733.1    121684    121740     113 KI270733.1    122136    122225
## 29 KI270733.1    121741    121751     112 KI270733.1    122136    122225
## 30 KI270733.1    166771    166804     100 KI270733.1    167218    167307
## 31          Y  12869925  12869974     102          Y  12537650  12860839
##          gene dist_bp
## 1  AL031737.1   15620
## 2   CTTNBP2NL    8317
## 3   CTTNBP2NL    8162
## 4   LINC02649       0
## 5     TCERG1L   35219
## 6     TCERG1L   35270
## 7     TCERG1L   35520
## 8     TMPRSS5   60251
## 9     TMPRSS5   60070
## 10   RNU6-70P    8122
## 11 FP671120.4       0
## 12 FP671120.4       0
## 13  MIR6724-2      13
## 14  MIR6724-2      70
## 15 FP236383.3       0
## 16 FP236383.3       0
## 17 FP236383.3       0
## 18     GRAMD4       0
## 19       BRD9       0
## 20   ANKRD33B       0
## 21 AC034228.3       0
## 22 AC034228.2       0
## 23      ELMO1       0
## 24      ELMO1       0
## 25       DMTN       0
## 26 AL592188.2     397
## 27 AL592188.2     386
## 28 AL353644.1     397
## 29 AL353644.1     386
## 30 AL353644.2     415
## 31      USP9Y    9087
## 
## $pool23
##           chr     start       end n_reads      chr.1   start.1     end.1
## 1           1  18611255  18611344     564          1  18595414  18595636
## 2          10   6307512   6307583     246         10   6271169   6353827
## 3          10  70005108  70005147     117         10  69994276  70019496
## 4          10  70005357  70005404     117         10  69994276  70019496
## 5          10 131346939 131346970     238         10 131092391 131311721
## 6          10 131346990 131347017     318         10 131092391 131311721
## 7          10 131347240 131347276     554         10 131092391 131311721
## 8          11  80568673  80568788     280         11  80527960  80528066
## 9          11  80568796  80568810     275         11  80527960  80528066
## 10         16  14989694  14989865     108         16  14974591  15139339
## 11         16  14989694  14989865     108         16  14988259  14990160
## 12         22  46679451  46679485     400         22  46576012  46679790
## 13          4   8288864   8288929     125          4   8269754   8307098
## 14          5    865245    865502    1566          5    850291    892801
## 15          5  10649438  10649513    8843          5  10564070  10657816
## 16          5 131945721 131945786    1012          5 131807143 132011637
## 17          5 131945721 131945786    1012          5 131944408 131968220
## 18          5 131945789 131945799    1003          5 131807143 132011637
## 19          5 131945789 131945799    1003          5 131944408 131968220
## 20          7  37256513  37256549     206          7  36852906  37449223
## 21          7  37256753  37256803     202          7  36852906  37449223
## 22          8  22055623  22055743    1943          8  22048995  22082527
## 23 KI270733.1    133694    133777     106 KI270733.1    128877    129029
## 24 KI270733.1    178774    178856     105 KI270733.1    173956    174108
## 25          Y  12869910  12869975     183          Y  12537650  12860839
##          gene dist_bp
## 1  AL031737.1   15620
## 2   LINC02649       0
## 3   LINC02636       0
## 4   LINC02636       0
## 5     TCERG1L   35219
## 6     TCERG1L   35270
## 7     TCERG1L   35520
## 8   RNU6-544P   40608
## 9   RNU6-544P   40731
## 10     PDXDC1       0
## 11 AC138932.2       0
## 12     GRAMD4       0
## 13      HTRA3       0
## 14       BRD9       0
## 15   ANKRD33B       0
## 16 AC034228.3       0
## 17 AC034228.2       0
## 18 AC034228.3       0
## 19 AC034228.2       0
## 20      ELMO1       0
## 21      ELMO1       0
## 22       DMTN       0
## 23  RNA5-8SN4    4666
## 24  5_8S_rRNA    4667
## 25      USP9Y    9072
## 
## $pool24
##    chr     start       end n_reads chr.1   start.1     end.1        gene
## 1    1  43926216  43926323     356     1  43650149  43931014  AL451062.2
## 2    1  43926216  43926323     356     1  43705824  43931165     ST3GAL3
## 3   11  78417513  78417543     330    11  78215293  78418348        GAB2
## 4   11  78417513  78417543     330    11  78324758  78444049  AP003086.1
## 5   12 105330765 105330791     503    12 105235290 105396097    C12orf75
## 6   16  14989617  14989628     109    16  14974591  15139339      PDXDC1
## 7   16  14989617  14989628     109    16  14988259  14990160  AC138932.2
## 8   16  14989629  14989930     219    16  14974591  15139339      PDXDC1
## 9   16  14989629  14989930     219    16  14988259  14990160  AC138932.2
## 10  17   4550782   4550844     390    17   4538897   4555386     MYBBP1A
## 11  19  11551551  11551692     224    19  11551147  11559236       ELOF1
## 12  19  38326060  38326071     119    19  38319845  38332076       KCNK6
## 13  19  38326072  38326126     119    19  38319845  38332076       KCNK6
## 14  22  46679451  46679485     259    22  46576012  46679790      GRAMD4
## 15   4   8288864   8288951    1128     4   8269754   8307098       HTRA3
## 16   5    865245    865502    2330     5    850291    892801        BRD9
## 17   5  10649438  10649513    7273     5  10564070  10657816    ANKRD33B
## 18   5 131945721 131945786    1272     5 131807143 132011637  AC034228.3
## 19   5 131945721 131945786    1272     5 131944408 131968220  AC034228.2
## 20   5 131945789 131945799    1251     5 131807143 132011637  AC034228.3
## 21   5 131945789 131945799    1251     5 131944408 131968220  AC034228.2
## 22   8   1974504   1974546     185     8   1971153   1974637  AC019257.1
## 23   8   1974504   1974546     185     8   1971397   1976478 KBTBD11-OT1
## 24   8   1974504   1974546     185     8   1973677   2006936     KBTBD11
## 25   8  22055623  22055726     870     8  22048995  22082527        DMTN
## 26   8  22055727  22055743     862     8  22048995  22082527        DMTN
##    dist_bp
## 1        0
## 2        0
## 3        0
## 4        0
## 5        0
## 6        0
## 7        0
## 8        0
## 9        0
## 10       0
## 11       0
## 12       0
## 13       0
## 14       0
## 15       0
## 16       0
## 17       0
## 18       0
## 19       0
## 20       0
## 21       0
## 22       0
## 23       0
## 24       0
## 25       0
## 26       0
## 
## $pool3
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611336     529     1  18595414  18595636 AL031737.1   15620
## 2   10   6307526   6307583     419    10   6271169   6353827  LINC02649       0
## 3   16  15177391  15177437     110    16  15154903  15157020 AC126763.1   20372
## 4   17   4550782   4550844     150    17   4538897   4555386    MYBBP1A       0
## 5   17  62060954  62061019     288    17  61942605  62065278      MED13       0
## 6   17  65561479  65561525     948    17  65528563  65561648      AXIN2       0
## 7   17  65561479  65561525     948    17  65538102  65641033 AC004805.1       0
## 8   22  46679451  46679485     482    22  46576012  46679790     GRAMD4       0
## 9    4   8288865   8288898     112     4   8269754   8307098      HTRA3       0
## 10   5    865245    865502     834     5    850291    892801       BRD9       0
## 11   5  10649438  10649513   16465     5  10564070  10657816   ANKRD33B       0
## 12   5 131945721 131945786    1525     5 131807143 132011637 AC034228.3       0
## 13   5 131945721 131945786    1525     5 131944408 131968220 AC034228.2       0
## 14   5 131945789 131945799    1495     5 131807143 132011637 AC034228.3       0
## 15   5 131945789 131945799    1495     5 131944408 131968220 AC034228.2       0
## 16   8  22055623  22055743    2893     8  22048995  22082527       DMTN       0
## 17   8 144560678 144560685     111     8 144529179 144605816   ARHGAP39       0
## 18   8 144560686 144560738     111     8 144529179 144605816   ARHGAP39       0
## 19   X 119552588 119552625     136     X 119538149 119565409    CXorf56       0
## 20   X 119552627 119552635     136     X 119538149 119565409    CXorf56       0
## 21   Y  12869918  12869975     288     Y  12537650  12860839      USP9Y    9080
## 
## $pool4
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611336     315     1  18595414  18595636 AL031737.1   15620
## 2   10   6307508   6307583     230    10   6271169   6353827  LINC02649       0
## 3   10 103584482 103584577     117    10 103493979 103592552     NEURL1       0
## 4   16  14989617  14989628     107    16  14974591  15139339     PDXDC1       0
## 5   16  14989617  14989628     107    16  14988259  14990160 AC138932.2       0
## 6   16  14989629  14989930     213    16  14974591  15139339     PDXDC1       0
## 7   16  14989629  14989930     213    16  14988259  14990160 AC138932.2       0
## 8   22  46679451  46679485     238    22  46576012  46679790     GRAMD4       0
## 9    4   3611860   3611931     106     4   3633029   3633975 AL121796.1   21099
## 10   4   8288864   8288951    2350     4   8269754   8307098      HTRA3       0
## 11   5    865245    865502    1249     5    850291    892801       BRD9       0
## 12   5  10649438  10649513   11784     5  10564070  10657816   ANKRD33B       0
## 13   5  66573511  66573558     130     5  66572057  66572546    PPIAP78     966
## 14   5 131945721 131945800    2391     5 131807143 132011637 AC034228.3       0
## 15   5 131945721 131945800    2391     5 131944408 131968220 AC034228.2       0
## 16   6 104424412 104424455     127     6 104487095 104528158 AL357522.1   62641
## 17   8  22055623  22055743    3973     8  22048995  22082527       DMTN       0
## 
## $pool5
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611340     239     1  18595414  18595636 AL031737.1   15620
## 2    1 112387835 112387898     195     1 112396214 112463456  CTTNBP2NL    8317
## 3    1 112387982 112388053     195     1 112396214 112463456  CTTNBP2NL    8162
## 4   10 131346939 131346970     195    10 131092391 131311721    TCERG1L   35219
## 5   10 131346990 131347017     236    10 131092391 131311721    TCERG1L   35270
## 6   10 131347240 131347276     424    10 131092391 131311721    TCERG1L   35520
## 7   11 113627262 113627297     190    11 113687547 113706373    TMPRSS5   60251
## 8   11 113627447 113627478     187    11 113687547 113706373    TMPRSS5   60070
## 9   15  76814085  76814137     174    15  76347904  76905444     SCAPER       0
## 10  18   3412110   3412182     212    18   3411608   3459978      TGIF1       0
## 11  18  80001920  80001951     100    18  79970813  80033949     TXNL4A       0
## 12  21  28059665  28059710     108    21  28048404  28137611  LINC01697       0
## 13  22  46679451  46679485     241    22  46576012  46679790     GRAMD4       0
## 14   5    865245    865502     901     5    850291    892801       BRD9       0
## 15   5  10649438  10649513   13490     5  10564070  10657816   ANKRD33B       0
## 16   5  21485325  21485356     102     5  21341833  21589372     GUSBP1       0
## 17   5  34188811  34188842     105     5  34164698  34244796 AC138409.2       0
## 18   5  69652010  69652055     104     5  69639459  69679259     GUSBP3       0
## 19   5  69904397  69904442     101     5  69875271  69920867    GUSBP13       0
## 20   5  70213701  70213746     106     5  70197255  70207745 AC138866.1    5957
## 21   5  70528127  70528172     109     5  70516387  70555266    GUSBP15       0
## 22   5  71232086  71232131     111     5  71220356  71259238    GUSBP17       0
## 23   5 131945721 131945799    2036     5 131807143 132011637 AC034228.3       0
## 24   5 131945721 131945799    2036     5 131944408 131968220 AC034228.2       0
## 25   6 124862224 124862255     100     6 124644434 124963165 RNF217-AS1       0
## 26   8  22055623  22055743    2879     8  22048995  22082527       DMTN       0
## 27   X  13044583  13044596     458     X  13035617  13044682      FAM9C       0
## 28   X  13044599  13044672     465     X  13035617  13044682      FAM9C       0
## 29   Y  12869916  12869975     108     Y  12537650  12860839      USP9Y    9078
## 
## $pool6
##    chr     start       end n_reads chr.1   start.1     end.1        gene
## 1    1  18611255  18611340     612     1  18595414  18595636  AL031737.1
## 2   10   6307518   6307583     297    10   6271169   6353827   LINC02649
## 3   10 132135162 132135199     150    10 132036336 132184858     JAKMIP3
## 4   12  12058886  12058925     267    12  12049844  12211084     BCL2L14
## 5   17   4550782   4550844     147    17   4538897   4555386     MYBBP1A
## 6   18  58646198  58646240     342    18  58659858  58660524  AC104971.3
## 7   19  28435207  28435249     283    19  28435388  28727680  AC005394.2
## 8   20    897327    897368     345    20    869900    916334      ANGPT4
## 9   20  29876340  29876455     143    20  29874059  29874177   RNA5SP532
## 10  22  29788944  29789092     139    22  29788609  29838304       ASCC2
## 11  22  29789093  29789115     136    22  29788609  29838304       ASCC2
## 12  22  29789117  29789131     133    22  29788609  29838304       ASCC2
## 13  22  46679451  46679485    1507    22  46576012  46679790      GRAMD4
## 14   3  72680749  72680784     100     3  72691705  72691811   RNA5SP136
## 15   3 179525820 179525862     385     3 179562886 179588407      ACTL6A
## 16   4   8288864   8288951    5299     4   8269754   8307098       HTRA3
## 17   5    865245    865502    1982     5    850291    892801        BRD9
## 18   5  10649438  10649513   18147     5  10564070  10657816    ANKRD33B
## 19   5 131945721 131945799    2085     5 131807143 132011637  AC034228.3
## 20   5 131945721 131945799    2085     5 131944408 131968220  AC034228.2
## 21   7  30480049  30480091     261     7  30424527  30478784        NOD1
## 22   7 143105600 143105642     330     7 143132077 143139739         PIP
## 23   8   1974504   1974546     215     8   1971153   1974637  AC019257.1
## 24   8   1974504   1974546     215     8   1971397   1976478 KBTBD11-OT1
## 25   8   1974504   1974546     215     8   1973677   2006936     KBTBD11
## 26   8  22055623  22055743    5609     8  22048995  22082527        DMTN
## 27   8  41063496  41063528     184     8  41032892  41032998   RNU6-356P
## 28   8  81903427  81903469     321     8  81841952  81924348   LINC02235
## 29   9 136857998 136858033     398     9 136850943 136860799      MAMDC4
## 30   9 136858034 136858050     396     9 136850943 136860799      MAMDC4
## 31   X   3983551   3983596     614     X   3953056   3953561     RPL24P9
## 32   Y  12869914  12869975     309     Y  12537650  12860839       USP9Y
##    dist_bp
## 1    15620
## 2        0
## 3        0
## 4        0
## 5        0
## 6    13619
## 7      140
## 8        0
## 9     2164
## 10       0
## 11       0
## 12       0
## 13       0
## 14   10922
## 15   37025
## 16       0
## 17       0
## 18       0
## 19       0
## 20       0
## 21    1266
## 22   26436
## 23       0
## 24       0
## 25       0
## 26       0
## 27   30499
## 28       0
## 29       0
## 30       0
## 31   29991
## 32    9076
## 
## $pool7
##           chr     start       end n_reads      chr.1   start.1     end.1
## 1           1  18611255  18611308     156          1  18595414  18595636
## 2           1  53276939  53276983     309          1  53242364  53328469
## 3          10   6307534   6307583     201         10   6271169   6353827
## 4          10  10027960  10028013    2108         10  10058722  10063502
## 5          22  46679451  46679485    1565         22  46576012  46679790
## 6           4   8288864   8288951    2466          4   8269754   8307098
## 7           5    865245    865502     777          5    850291    892801
## 8           5   4384227   4384295     139          5   4436850   4440259
## 9           5  10649438  10649513    9655          5  10564070  10657816
## 10          5  66573511  66573558     116          5  66572057  66572546
## 11          5 131945721 131945786     682          5 131807143 132011637
## 12          5 131945721 131945786     682          5 131944408 131968220
## 13          5 131945789 131945799     669          5 131807143 132011637
## 14          5 131945789 131945799     669          5 131944408 131968220
## 15          6 104424412 104424455     132          6 104487095 104528158
## 16          8  22055623  22055743    2547          8  22048995  22082527
## 17 GL000225.1     53207     53255     514 GL000225.1    183252    183364
## 18          X  13044583  13044596     388          X  13035617  13044682
## 19          X  13044599  13044672     420          X  13035617  13044682
## 20          Y  12869918  12869975     223          Y  12537650  12860839
##          gene dist_bp
## 1  AL031737.1   15620
## 2        LRP8       0
## 3   LINC02649       0
## 4   LINC02670   30710
## 5      GRAMD4       0
## 6       HTRA3       0
## 7        BRD9       0
## 8  AC106799.3   52556
## 9    ANKRD33B       0
## 10    PPIAP78     966
## 11 AC034228.3       0
## 12 AC034228.2       0
## 13 AC034228.3       0
## 14 AC034228.2       0
## 15 AL357522.1   62641
## 16       DMTN       0
## 17         U2  129998
## 18      FAM9C       0
## 19      FAM9C       0
## 20      USP9Y    9080
## 
## $pool8
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611316     367     1  18595414  18595636 AL031737.1   15620
## 2    1 228610466 228610478     114     1 228610268 228610386     RNA5S1      81
## 3    1 228610482 228610537     114     1 228610268 228610386     RNA5S1      97
## 4    1 228612707 228612719     119     1 228612509 228612627     RNA5S2      81
## 5    1 228612723 228612778     120     1 228612509 228612627     RNA5S2      97
## 6    1 228614948 228614959     115     1 228614750 228614868     RNA5S3      81
## 7    1 228614964 228615019     116     1 228614750 228614868     RNA5S3      97
## 8    1 228619430 228619442     122     1 228619232 228619350     RNA5S5      81
## 9    1 228619446 228619501     122     1 228619232 228619350     RNA5S5      97
## 10   1 228626107 228626118     110     1 228625909 228626027     RNA5S8      81
## 11   1 228626123 228626178     111     1 228625909 228626027     RNA5S8      97
## 12   1 228628346 228628358     153     1 228628148 228628266     RNA5S9      81
## 13   1 228628362 228628417     153     1 228628148 228628266     RNA5S9      97
## 14   1 228630589 228630599     102     1 228630390 228630508    RNA5S10      82
## 15   1 228630604 228630657     102     1 228630390 228630508    RNA5S10      97
## 16   1 228632829 228632841     117     1 228632631 228632749    RNA5S11      81
## 17   1 228632845 228632900     117     1 228632631 228632749    RNA5S11      97
## 18   1 228635069 228635081     119     1 228634871 228634989    RNA5S12      81
## 19   1 228635085 228635140     120     1 228634871 228634989    RNA5S12      97
## 20   1 228637294 228637306     125     1 228637096 228637214    RNA5S13      81
## 21   1 228637310 228637365     128     1 228637096 228637214    RNA5S13      97
## 22   1 228639535 228639547     111     1 228639337 228639455    RNA5S14      81
## 23   1 228639551 228639606     111     1 228639337 228639455    RNA5S14      97
## 24   1 228641766 228641777     108     1 228641568 228641686    RNA5S15      81
## 25   1 228641782 228641837     108     1 228641568 228641686    RNA5S15      97
## 26   1 228644008 228644018     105     1 228643809 228643927    RNA5S16      82
## 27   1 228644023 228644078     106     1 228643809 228643927    RNA5S16      97
## 28   1 228646238 228646250     129     1 228646040 228646158    RNA5S17      81
## 29   1 228646254 228646309     129     1 228646040 228646158    RNA5S17      97
## 30  10   6307526   6307583     391    10   6271169   6353827  LINC02649       0
## 31  10 125774165 125774287     162    10 125753580 125775821      MMP21       0
## 32  10 125774290 125774307     162    10 125753580 125775821      MMP21       0
## 33  10 131346990 131347017     132    10 131092391 131311721    TCERG1L   35270
## 34  10 131347243 131347276     182    10 131092391 131311721    TCERG1L   35523
## 35  11   2457620   2457656    2155    11   2444684   2849105      KCNQ1       0
## 36  11  65786127  65786205     136    11  65787063  65797214      OVOL1     859
## 37  11 113627262 113627297     164    11 113687547 113706373    TMPRSS5   60251
## 38  11 113627447 113627478     164    11 113687547 113706373    TMPRSS5   60070
## 39  20  29411394  29411458     392    20  29410348  29411600    DUX4L34       0
## 40  22  46679451  46679485    1273    22  46576012  46679790     GRAMD4       0
## 41   4   8288864   8288951    3994     4   8269754   8307098      HTRA3       0
## 42   5    865245    865502     541     5    850291    892801       BRD9       0
## 43   5  10649438  10649513   17948     5  10564070  10657816   ANKRD33B       0
## 44   5 131945721 131945786    1027     5 131807143 132011637 AC034228.3       0
## 45   5 131945721 131945786    1027     5 131944408 131968220 AC034228.2       0
## 46   5 131945789 131945799    1010     5 131807143 132011637 AC034228.3       0
## 47   5 131945789 131945799    1010     5 131944408 131968220 AC034228.2       0
## 48   5 167774205 167774259     544     5 167284799 168264157      TENM2       0
## 49   7  37256513  37256549     121     7  36852906  37449223      ELMO1       0
## 50   7  37256669  37256708     118     7  36852906  37449223      ELMO1       0
## 51   8  22055623  22055743    3993     8  22048995  22082527       DMTN       0
## 52   Y  12869918  12869975     368     Y  12537650  12860839      USP9Y    9080
## 
## $pool9
##    chr     start       end n_reads chr.1   start.1     end.1       gene dist_bp
## 1    1  18611255  18611324     366     1  18595414  18595636 AL031737.1   15620
## 2   10   6307518   6307583     387    10   6271169   6353827  LINC02649       0
## 3   10 131346990 131347017     125    10 131092391 131311721    TCERG1L   35270
## 4   10 131347241 131347276     213    10 131092391 131311721    TCERG1L   35521
## 5   17  43665375  43665443     115    17  43640389  43661922      MEOX1    3454
## 6   22  46679451  46679485     136    22  46576012  46679790     GRAMD4       0
## 7    5    865245    865502    2334     5    850291    892801       BRD9       0
## 8    5  10649438  10649513    8206     5  10564070  10657816   ANKRD33B       0
## 9    5 131945721 131945786     780     5 131807143 132011637 AC034228.3       0
## 10   5 131945721 131945786     780     5 131944408 131968220 AC034228.2       0
## 11   5 131945789 131945799     774     5 131807143 132011637 AC034228.3       0
## 12   5 131945789 131945799     774     5 131944408 131968220 AC034228.2       0
## 13   7  37256513  37256549     257     7  36852906  37449223      ELMO1       0
## 14   7  37256753  37256803     256     7  36852906  37449223      ELMO1       0
## 15   8  22055623  22055743    3376     8  22048995  22082527       DMTN       0
## 16   9  31321373  31321440     119     9  31371611  31381490  LINC01243   50172
## 17   Y  12869910  12869975     374     Y  12537650  12860839      USP9Y    9072
## 
## $PoolM
##    chr     start       end n_reads chr.1   start.1     end.1         gene
## 1    1   5991850   5991895     119     1   5862811   5992473        NPHP4
## 2    1   5991850   5991895     119     1   5990927   6101193       KCNAB2
## 3    1 164321420 164321491     119     1 164343005 164343864     NMNAT1P2
## 4    1 168940009 168940047     384     1 168695874 169103276   AL135926.1
## 5    1 168940009 168940047     384     1 168903905 169087005    LINC00970
## 6    1 234742415 234742439    1097     1 234724042 234736720    LINC01132
## 7    1 240093617 240093698     148     1 240014348 240475187         FMN2
## 8   10   5813834   5813885     151    10   5765223   5842132         GDI2
## 9   10   5813887   5813902     150    10   5765223   5842132         GDI2
## 10  10  32347230  32347346     160    10  32267751  32378798         EPC1
## 11  10  93342741  93342782     187    10  93306429  93482334         MYOF
## 12  10 108862573 108862623    1565    10 108848186 108849561   MAPKAPK5P1
## 13  10 108862625 108862636    1551    10 108848186 108849561   MAPKAPK5P1
## 14  11  93330754  93330800     123    11  93329971  93438487        DEUP1
## 15  11 130916242 130916335     212    11 130866250 130916479        SNX19
## 16  12  47773188  47773214     382    12  47753916  47782751      SLC48A1
## 17  12  47773215  47773231     382    12  47753916  47782751      SLC48A1
## 18  12  64404619  64404626     174    12  64404392  64451125         XPOT
## 19  12  64404627  64404666     177    12  64404392  64451125         XPOT
## 20  12  64404670  64404681     175    12  64404392  64451125         XPOT
## 21  12 100372360 100372458     518    12 100357074 100422055      SLC17A8
## 22  12 105330759 105330791     831    12 105235290 105396097     C12orf75
## 23  12 118163439 118163472     262    12 118149801 118372907        TAOK3
## 24  15  80403871  80403944     491    15  80344853  80404214   AC016705.2
## 25  15  95066953  95067013    7909    15  94841059  95169864   AC087633.2
## 26  16  14989693  14989865     116    16  14974591  15139339       PDXDC1
## 27  16  14989693  14989865     116    16  14988259  14990160   AC138932.2
## 28  16  35639205  35639236     122    16  35636687  35645180     KIF18BP1
## 29  16  50708892  50708931     198    16  50693588  50734041         NOD2
## 30  16  62108333  62108393     242    16  61647242  62037035         CDH8
## 31  16  70251562  70251701     243    16  70246778  70251940       EXOSC6
## 32  16  78347038  78347078    2797    16  78099430  79212667         WWOX
## 33  17  13254784  13254854     276    17  13299184  13306771    LINC02093
## 34  17  15786192  15786281     179    17  15786618  15787575      MEIS3P1
## 35  18   9996768   9996808     935    18   9914016   9960021         VAPA
## 36  18  10590130  10590154    1098    18  10594590  10604798   AP001099.1
## 37  19   1600354   1600378    1123    19   1578339   1605445   AC005943.1
## 38  19   1600354   1600378    1123    19   1597169   1605473       UQCR11
## 39  19  48855456  48855480    1222    19  48837097  48868617      PLEKHA4
## 40   2  70477225  70477246     114     2  70447284  70554193         TGFA
## 41   2 111349875 111349923     120     2 111006015 111523376  MIR4435-2HG
## 42   2 119593691 119593715    1087     2 119544432 119662251      CFAP221
## 43   3  54205770  54205813     266     3  54122547  55074557     CACNA2D3
## 44   3  60181850  60181884     136     3  59747277  61251459         FHIT
## 45   3 138508460 138508543     879     3 138494344 138594538        CEP70
## 46   4   8288864   8288951     810     4   8269754   8307098        HTRA3
## 47   4  18051824  18051868     315     4  17841199  18021876        LCORL
## 48   4 122261613 122261700     844     4 122152331 122362758     KIAA1109
## 49   5  10649439  10649513    1822     5  10564070  10657816     ANKRD33B
## 50   5  96294197  96294227    2278     5  95962001  96631085   AC104123.1
## 51   5 115668895 115668939     139     5 115691462 115692167   AC008549.2
## 52   5 131945721 131945786     511     5 131807143 132011637   AC034228.3
## 53   5 131945721 131945786     511     5 131944408 131968220   AC034228.2
## 54   5 131945789 131945799     502     5 131807143 132011637   AC034228.3
## 55   5 131945789 131945799     502     5 131944408 131968220   AC034228.2
## 56   6  36461862  36461889     318     6  36442767  36491143       KCTD20
## 57   6  39792402  39792463     228     6  39792298  39904877        DAAM2
## 58   6  99568568  99568581     304     6  99520976  99589899        TSTD3
## 59   6  99568568  99568581     304     6  99542387  99568825         CCNC
## 60   6  99568582  99568627     309     6  99520976  99589899        TSTD3
## 61   6  99568582  99568627     309     6  99542387  99568825         CCNC
## 62   7 148667487 148667528     114     7 148649547 148650240   AC005229.2
## 63   8   1974504   1974546     414     8   1971153   1974637   AC019257.1
## 64   8   1974504   1974546     414     8   1971397   1976478  KBTBD11-OT1
## 65   8   1974504   1974546     414     8   1973677   2006936      KBTBD11
## 66   8   4909665   4909688     148     8   2935353   4994972        CSMD1
## 67   8  22055623  22055726     220     8  22048995  22082527         DMTN
## 68   8  22055727  22055743     219     8  22048995  22082527         DMTN
## 69   8  30812217  30812293     326     8  30774457  30814314       PPP2CB
## 70   8  66712550  66712702    3980     8  66667596  66860472 C8orf44-SGK3
## 71   8 109465537 109465573     284     8 109362461 109537207      PKHD1L1
## 72   9     76145     76236     360     9     72670     89850   PGM5P3-AS1
## 73   9  36136741  36136851     380     9  36136536  36163913       GLIPR2
## 74   9  68354257  68354348     360     9  68328308  68531061         PGM5
## 75   9  68354257  68354348     360     9  68353614  68357893     PGM5-AS1
## 76   X   5359719   5359783     196     X   5410122   5410251   AC095353.1
## 77   X  44874005  44874064     202     X  44873188  45112779        KDM6A
##    dist_bp
## 1        0
## 2        0
## 3    21515
## 4        0
## 5        0
## 6     5696
## 7        0
## 8        0
## 9        0
## 10       0
## 11       0
## 12   13013
## 13   13065
## 14       0
## 15       0
## 16       0
## 17       0
## 18       0
## 19       0
## 20       0
## 21       0
## 22       0
## 23       0
## 24       0
## 25       0
## 26       0
## 27       0
## 28       0
## 29       0
## 30   71299
## 31       0
## 32       0
## 33   44331
## 34     338
## 35   36748
## 36    4437
## 37       0
## 38       0
## 39       0
## 40       0
## 41       0
## 42       0
## 43       0
## 44       0
## 45       0
## 46       0
## 47   29949
## 48       0
## 49       0
## 50       0
## 51   22524
## 52       0
## 53       0
## 54       0
## 55       0
## 56       0
## 57       0
## 58       0
## 59       0
## 60       0
## 61       0
## 62   17248
## 63       0
## 64       0
## 65       0
## 66       0
## 67       0
## 68       0
## 69       0
## 70       0
## 71       0
## 72       0
## 73       0
## 74       0
## 75       0
## 76   50340
## 77       0
## 
## $PoolMM
##    chr     start       end n_reads chr.1   start.1     end.1        gene
## 1    1 234690965 234690994     120     1 234669523 234696153  AL160408.3
## 2    1 234742415 234742439    3703     1 234724042 234736720   LINC01132
## 3   10  54011707  54011774     169    10  53802771  55627942      PCDH15
## 4   10  70378639  70378682     120    10  70298970  70382650      LRRC20
## 5   10 112050459 112050465     713    10 111787233 111989909  AL136119.1
## 6   10 112050466 112050494     717    10 111787233 111989909  AL136119.1
## 7   11  35003588  35003634     232    11  34915829  35020591        PDHX
## 8   11  65067931  65067986     185    11  65066300  65084164       CDCA5
## 9   11  69974845  69974899     134    11  69985876  70015815  AP003555.2
## 10  12  55273510  55273577     140    12  55262539  55263431     OR6C69P
## 11  12 105330759 105330791    2542    12 105235290 105396097    C12orf75
## 12  13  41924412  41924449     168    13  41566835  41961120        VWA8
## 13  14  36580240  36580293    1203    14  36320753  36656163  AL132857.1
## 14  14  36580240  36580293    1203    14  36580004  36582614      NKX2-8
## 15  14  36580295  36580310    1181    14  36320753  36656163  AL132857.1
## 16  14  36580295  36580310    1181    14  36580004  36582614      NKX2-8
## 17  15  26275973  26276063     226    15  26261669  26265918  AC012060.1
## 18  18  10590130  10590154    3981    18  10594590  10604798  AP001099.1
## 19  19   1600354   1600378    3820    19   1578339   1605445  AC005943.1
## 20  19   1600354   1600378    3820    19   1597169   1605473      UQCR11
## 21  19  48855456  48855480    4032    19  48837097  48868617     PLEKHA4
## 22   2  10399589  10399610     118     2  10302889  10427617      HPCAL1
## 23   2  30334177  30334230     999     2  30343222  30348298  AC109642.1
## 24   2  70477216  70477246     868     2  70447284  70554193        TGFA
## 25   2  88069490  88069519    2336     2  88067825  88113384       SMYD1
## 26   2 119593691 119593715    3805     2 119544432 119662251     CFAP221
## 27   2 149038924 149038977     633     2 149038107 149215262      LYPD6B
## 28   4  13436379  13436398     116     4  13361354  13484365       RAB28
## 29   4  13436399  13436471     116     4  13361354  13484365       RAB28
## 30   4  18671384  18671419     132     4  18418662  18888662  AC093898.1
## 31   4  78125849  78125923     122     4  78057323  78544269       FRAS1
## 32   5  84522157  84522201     582     5  84382424  84490765    EDIL3-DT
## 33   5 125362225 125362268     134     5 124808981 125602227   LINC02240
## 34   5 125362225 125362268     134     5 125333369 126368755  AC116362.1
## 35   5 143586716 143586775    2773     5 143531331 143598434  AC016598.2
## 36   6  54751950  54752026     468     6  54770583  54771134      KRASP1
## 37   6 125050045 125050092     272     6 124962545 125092633      RNF217
## 38   6 162134756 162134804     329     6 161347417 162727775        PRKN
## 39   7  45596896  45596960     127     7  45574140  45723116       ADCY1
## 40   7 147628581 147628618     122     7 146116002 148420998     CNTNAP2
## 41   8   1974504   1974546    1773     8   1971153   1974637  AC019257.1
## 42   8   1974504   1974546    1773     8   1971397   1976478 KBTBD11-OT1
## 43   8   1974504   1974546    1773     8   1973677   2006936     KBTBD11
## 44   X  78458592  78458645     382     X  78519593  78520186    HMGN1P34
##    dist_bp
## 1        0
## 2     5696
## 3        0
## 4        0
## 5    60551
## 6    60558
## 7        0
## 8        0
## 9    10978
## 10   10080
## 11       0
## 12       0
## 13       0
## 14       0
## 15       0
## 16       0
## 17   10056
## 18    4437
## 19       0
## 20       0
## 21       0
## 22       0
## 23    8993
## 24       0
## 25       0
## 26       0
## 27       0
## 28       0
## 29       0
## 30       0
## 31       0
## 32   31393
## 33       0
## 34       0
## 35       0
## 36   18558
## 37       0
## 38       0
## 39       0
## 40       0
## 41       0
## 42       0
## 43       0
## 44   60949
## 
## $Undetermined
##    chr     start       end n_reads chr.1   start.1     end.1         gene
## 1    1  18611255  18611326     275     1  18595414  18595636   AL031737.1
## 2   10   6307518   6307583     307    10   6271169   6353827    LINC02649
## 3   10  10027960  10028013     152    10  10058722  10063502    LINC02670
## 4   10 100122122 100122149     142    10 100105754 100140151     CYP2C23P
## 5   10 100122170 100122185     120    10 100105754 100140151     CYP2C23P
## 6   15  95066953  95067013     227    15  94841059  95169864   AC087633.2
## 7   16  14989690  14989868     156    16  14974591  15139339       PDXDC1
## 8   16  14989690  14989868     156    16  14988259  14990160   AC138932.2
## 9   19  35358874  35359135    3973    19  35358460  35360489        FFAR3
## 10  19  35371343  35371604    3969    19  35370929  35372962        GPR42
## 11   2  32916232  32916632    1964     2  32825359  32926693    LINC00486
## 12  22  46679451  46679485     299    22  46576012  46679790       GRAMD4
## 13   3  60181850  60181902     178     3  59747277  61251459         FHIT
## 14   4   8288864   8288955    2094     4   8269754   8307098        HTRA3
## 15   5    865245    865502    2611     5    850291    892801         BRD9
## 16   5  10649430  10649514   16571     5  10564070  10657816     ANKRD33B
## 17   5 119023122 119023140     150     5 119006347 119070902   AC008629.1
## 18   5 119023143 119023175     150     5 119006347 119070902   AC008629.1
## 19   5 131945721 131945788    1194     5 131807143 132011637   AC034228.3
## 20   5 131945721 131945788    1194     5 131944408 131968220   AC034228.2
## 21   5 131945789 131945799    1078     5 131807143 132011637   AC034228.3
## 22   5 131945789 131945799    1078     5 131944408 131968220   AC034228.2
## 23   5 143586716 143586735     105     5 143531331 143598434   AC016598.2
## 24   5 143586736 143586766     105     5 143531331 143598434   AC016598.2
## 25   6  54725892  54725921     239     6  54770583  54771134       KRASP1
## 26   6  54725998  54726020     239     6  54770583  54771134       KRASP1
## 27   8  22055623  22055743    3883     8  22048995  22082527         DMTN
## 28   8  66712550  66712695     188     8  66667596  66860472 C8orf44-SGK3
## 29   8  66712696  66712702     181     8  66667596  66860472 C8orf44-SGK3
## 30   X  82446629  82446671     185     X  82497669  82497924      EIF3JP1
## 31   X  82446673  82446687     183     X  82497669  82497924      EIF3JP1
## 32   Y  12869918  12869975     178     Y  12537650  12860839        USP9Y
##    dist_bp
## 1    15620
## 2        0
## 3    30710
## 4        0
## 5        0
## 6        0
## 7        0
## 8        0
## 9        0
## 10       0
## 11       0
## 12       0
## 13       0
## 14       0
## 15       0
## 16       0
## 17       0
## 18       0
## 19       0
## 20       0
## 21       0
## 22       0
## 23       0
## 24       0
## 25   44663
## 26   44564
## 27       0
## 28       0
## 29       0
## 30   50999
## 31   50983
## 32    9080

Now we can look at the sequence of these off-target regions. Lower case indicates that the sequence was repeat-masked.

myfiles <- list.files("fastq/",pattern=".bedgraph.offtarget.fa$",full.names=TRUE)

oft2 <- lapply(myfiles, function(x)  {
  y <- readLines(x)
  n=length(y)
  if(n>0){
    seq <- y[(1:(n/2))*2]
    names(seq) <- y[((1:(n/2))*2)-1]
    seq  
  }
})

names(oft2) <- gsub(".bam.bedgraph.offtarget.fa","",gsub("fastq//","",myfiles))

oft2
## $`101-1023`
##                                                                             >19:35358874-35358981 27777_107bp 
## "ACCAGTGGCCACCACCATGGATACAGGCCCCGACCAGTCCTACTTCTCCGGCAATCACTGGTTCGTCTTCTCGGTGTACCTTCTCACTTTCCTGGTGGGGCTCCCCC" 
##                                                                             >19:35371343-35371444 27968_101bp 
##       "ACCAGTGGCCACCACCATGGATACAGGCCCCGACCAGTCCTACTTCTCCGGCAATCACTGGTTCGTCTTCTCGGTGTACCTTCTCACTTTCCTGGTGGGGC" 
## 
## $`185-1135`
##                                                                                                                                                            >19:35358949-35359135 24019_186bp 
## "GTACCTTCTCACTTTCCTGGTGGGGCTCCCCCTCAACCTGCTGGCCCTGGTGGTCTTCGTGGGCAAGCTGCAGCGCCGCCCGGTGGCCGTGGACGTGCTCCTGCTCAACCTGACCGCCTCGGACCTGCTCCTGCTGCTGTTCCTGCCTTTCCGCATGGTGGAGGCAGCCAATGGCATGCACTGGCC" 
##                                                                                                                                                            >19:35371418-35371604 24643_186bp 
## "GTACCTTCTCACTTTCCTGGTGGGGCTCCCCCTCAACCTGCTGGCCCTGGTGGTCTTCGTGGGCAAGCTGCGGTGCCGCCCGGTGGCCGTGGACGTGCTCCTGCTCAACCTGACCGCCTCGGACCTGCTCCTGCTGCTGTTCCTGCCTTTCCGCATGGTGGAGGCAGCCAATGGCATGCACTGGCC" 
##                                                                                                                                                              >6:158378467-158378509 113_42bp 
##                                                                                                                                                 "ttttttttttttttttttggtgggggtgggggtgggagatgg" 
## 
## $`7185`
##                                                                                                                                                                   >19:35358949-35359142 20615_193bp 
## "GTACCTTCTCACTTTCCTGGTGGGGCTCCCCCTCAACCTGCTGGCCCTGGTGGTCTTCGTGGGCAAGCTGCAGCGCCGCCCGGTGGCCGTGGACGTGCTCCTGCTCAACCTGACCGCCTCGGACCTGCTCCTGCTGCTGTTCCTGCCTTTCCGCATGGTGGAGGCAGCCAATGGCATGCACTGGCCCCTGCCC" 
##                                                                                                                                                                   >19:35371418-35371611 19032_193bp 
## "GTACCTTCTCACTTTCCTGGTGGGGCTCCCCCTCAACCTGCTGGCCCTGGTGGTCTTCGTGGGCAAGCTGCGGTGCCGCCCGGTGGCCGTGGACGTGCTCCTGCTCAACCTGACCGCCTCGGACCTGCTCCTGCTGCTGTTCCTGCCTTTCCGCATGGTGGAGGCAGCCAATGGCATGCACTGGCCCCTGCCC" 
##                                                                                                                                                                     >2:152619971-152620002 102_31bp 
##                                                                                                                                                                   "CACTGGCCCCACCGAGAGAATGGAAGAGAGA" 
##                                                                                                                                                                       >7:39369845-39369878 156_33bp 
##                                                                                                                                                                 "gcatttttttttttttttggtgggggtggttag" 
##                                                                                                                                                                     >X:112340564-112340598 109_34bp 
##                                                                                                                                                                "TTATCTTTTCATCTTTTCGGCGGGGGTGGGGAGG" 
## 
## $Neg
## NULL
## 
## $NTC
## NULL
## 
## $pool1
##                                                                                                                                                                                                                                       >1:18611255-18611316 259_61bp 
##                                                                                                                                                                                                     "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                     >1:162034657-162034667 417_10bp 
##                                                                                                                                                                                                                                                        "ttagctcgta" 
##                                                                                                                                                                                                                                     >1:162034670-162034712 418_42bp 
##                                                                                                                                                                                                                        "aaggaaatggaggcagacagctggactaacttgctcaaggac" 
##                                                                                                                                                                                                                                        >10:6307526-6307583 195_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                      >11:65786127-65786205 111_78bp 
##                                                                                                                                                                                    "GGTGGCCGCAGCAGGGCAAAGGCGGCTGAGCCTTTCCCGGTCTGAGGTCCCCAGCCCTCCGCGCTCCACCAGCCTGGC" 
##                                                                                                                                                                                                                                        >17:4550782-4550844 593_62bp 
##                                                                                                                                                                                                    "gggaccaaaaacaaccacctctcacgcgcttactcagtgccagcacccgcgctccgcctttt" 
##                                                                                                                                                                                                                                      >19:13908861-13908908 118_47bp 
##                                                                                                                                                                                                                   "gcttccttctttttttccttccttccctccttcctccctccctctct" 
##                                                                                                                                                                                                                                       >2:35765764-35765776 145_12bp 
##                                                                                                                                                                                                                                                      "CTCAGTAAACAC" 
##                                                                                                                                                                                                                                       >2:35765778-35765802 146_24bp 
##                                                                                                                                                                                                                                          "AACTAGAGAGGCCGACTGTGCCTC" 
##                                                                                                                                                                                                                                       >2:35765803-35765822 146_19bp 
##                                                                                                                                                                                                                                               "AACTTCTGTTTGAGATTTG" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 216_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                      >3:60181850-60181902 4490_52bp 
##                                                                                                                                                                                                              "TCTGACTCCAAAAGAAATGGAGGTACACCCTCCTATATATATCTCTACCTGT" 
##                                                                                                                                                                                                                                     >3:186110029-186110063 153_34bp 
##                                                                                                                                                                                                                                "CCTCCGAAACGGGCATGCAGACTCAGACTTTTTG" 
##                                                                                                                                                                                                                                     >3:186110064-186110092 153_28bp 
##                                                                                                                                                                                                                                      "CTCCCTCCCCGGGCTGCTTGTTTTCCAT" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 2355_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                          >5:865245-865502 767_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 15302_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:119023122-119023140 4411_18bp 
##                                                                                                                                                                                                                                                "ttaactttgaaaacaatc" 
##                                                                                                                                                                                                                                    >5:119023143-119023175 4421_32bp 
##                                                                                                                                                                                                                                  "tgaggtacagttggccctccttatctataagt" 
##                                                                                                                                                                                                                                     >5:131945721-131945786 896_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                     >5:131945789-131945799 887_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4150_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >8:39240838-39240870 693_32bp 
##                                                                                                                                                                                                                                  "CAGcccaaatctcatgtcctcacatttcaaaa" 
##                                                                                                                                                                                                                                       >X:13044583-13044596 167_13bp 
##                                                                                                                                                                                                                                                     "TGGCACCGCGAAG" 
##                                                                                                                                                                                                                                       >X:13044599-13044672 174_73bp 
##                                                                                                                                                                                         "CTCCGAGGGCCTGGGTCCTCTGTTCTCACGAGAGCAGCAGCCGCCCCGGCTGCCCGCGCTCCTCGCTGATTGG" 
##                                                                                                                                                                                                                                       >Y:12869918-12869975 222_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool10
##                                                                                                                                                                                                                                     >1:234742415-234742439 763_24bp 
##                                                                                                                                                                                                                                          "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                                                                                                      >10:10027960-10028013 239_53bp 
##                                                                                                                                                                                                             "cagaaatagaggggcccaagcaagggattgcaactcaatttcaaaaacttctg" 
##                                                                                                                                                                                                                                    >12:105330759-105330791 224_32bp 
##                                                                                                                                                                                                                                  "CCCCACTCGGTTCCTGGCCCCTCGCGGCCCCG" 
##                                                                                                                                                                                                                                     >16:14989690-14989869 168_179bp 
##                                                                               "AGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAG" 
##                                                                                                                                                                                                                                      >18:10590130-10590154 759_24bp 
##                                                                                                                                                                                                                                          "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                                                                                                     >18:37891155-37891201 3213_46bp 
##                                                                                                                                                                                                                    "CTCCTGAAATCCTAAATCTCATTATCTTGCCTGTAGGTCTGGGTTG" 
##                                                                                                                                                                                                                                        >19:1600354-1600378 708_24bp 
##                                                                                                                                                                                                                                          "aggcgcccgtcactgcgcctggct" 
##                                                                                                                                                                                                                                      >19:38326060-38326071 139_11bp 
##                                                                                                                                                                                                                                                       "tcactgacaga" 
##                                                                                                                                                                                                                                      >19:38326072-38326126 140_54bp 
##                                                                                                                                                                                                            "ggagtgcggcatgagtgacgagggcgtcagggatgaaggcaaggctcttggcct" 
##                                                                                                                                                                                                                                      >19:46791472-46791496 228_24bp 
##                                                                                                                                                                                                                                          "agttgggcgtggtggcgggcggct" 
##                                                                                                                                                                                                                                      >19:48855456-48855480 706_24bp 
##                                                                                                                                                                                                                                          "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                                                                                                     >2:119593691-119593715 682_24bp 
##                                                                                                                                                                                                                                          "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 211_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 3647_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                      >4:78422580-78422696 168_116bp 
##                                                                                                                                              "gagaatgtgtccttgtgtctgaaatgtgaagggtcaggcagagcagggatgcatctggtgggagagacagaggccatacctgacagaccctcgaagcctgtaaggatttgggttgt" 
##                                                                                                                                                                                                                                       >4:78422698-78422709 163_11bp 
##                                                                                                                                                                                                                                                       "tcccaacatca" 
##                                                                                                                                                                                                                                         >5:865245-865502 1648_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                      >5:10649438-10649513 6749_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945786 1352_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                    >5:131945788-131945799 1328_11bp 
##                                                                                                                                                                                                                                                       "GCGCAGGTTCC" 
##                                                                                                                                                                                                                                       >7:86652471-86652495 233_24bp 
##                                                                                                                                                                                                                                          "agccgcccgccaccacgcccaact" 
##                                                                                                                                                                                                                                        >8:1974504-1974546 2771_42bp 
##                                                                                                                                                                                                                        "CCCTGGGGAGGGGAGCGCGGCCCTTGGTCCTCCGCCGCTGCG" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 3445_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
## 
## $pool11
##                                                                                                                                                                                                                             >4:8288864-8288951 403_87bp 
##                                                                                                                                                               "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                              >5:865245-865490 213_245bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCC" 
##                                                                                                                                                                                                                               >5:865491-865502 113_11bp 
##                                                                                                                                                                                                                                           "CCTGTGCTTCG" 
##                                                                                                                                                                                                                           >5:10649439-10649513 955_74bp 
##                                                                                                                                                                            "GGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                          >8:22055623-22055726 402_103bp 
##                                                                                                                                               "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCT" 
##                                                                                                                                                                                                                           >8:22055727-22055743 401_16bp 
##                                                                                                                                                                                                                                      "CCTTCTCTCTGGAGCC" 
## 
## $pool12
##                                                                                                                                                                                                                                      >1:18611255-18611340 1032_85bp 
##                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                       >1:58306257-58306325 156_68bp 
##                                                                                                                                                                                              "AGTTCAGTGGGGAAGGAGGAAGGAGGAAAAGGAGAACTGGAAGGGGCAAGGTGAAATTTGGGGGAGGA" 
##                                                                                                                                                                                                                                     >1:241065370-241065403 653_33bp 
##                                                                                                                                                                                                                                 "CCAAAATTTACCCCCACCCCTTCCAAATTCTGC" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 670_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                      >10:70183632-70183662 141_30bp 
##                                                                                                                                                                                                                                    "gagaaggaggaaggaaggaaggaaggaaAA" 
##                                                                                                                                                                                                                                      >10:83229789-83229800 316_11bp 
##                                                                                                                                                                                                                                                       "agcaagaggct" 
##                                                                                                                                                                                                                                      >10:83229801-83229848 363_47bp 
##                                                                                                                                                                                                                   "aaactaggaaaggcacccactcccccgactctgcctccatttcattt" 
##                                                                                                                                                                                                                                    >10:100122122-100122149 289_27bp 
##                                                                                                                                                                                                                                       "agggagggaggaaggaaggaaggaagg" 
##                                                                                                                                                                                                                                    >10:100122170-100122193 284_23bp 
##                                                                                                                                                                                                                                           "aggaaggaaggaaggaaaatttg" 
##                                                                                                                                                                                                                                      >11:25874404-25874455 106_51bp 
##                                                                                                                                                                                                               "ACCGCTACAAAACAGACCTGAGGCAGATCCTGATGGTTGCTGGCTTTCTTT" 
##                                                                                                                                                                                                                                      >11:65726854-65726937 348_83bp 
##                                                                                                                                                                               "aaacaagggctgACCTAGAGGAAGCTTCTCCATCCTTGAATCTACATCTGGTTCGGCCTGCCTACCTCCACTCCTGCCTCCAT" 
##                                                                                                                                                                                                                                      >15:20074892-20074922 223_30bp 
##                                                                                                                                                                                                                                    "ttcatggcctttgggttgcttctatctctt" 
##                                                                                                                                                                                                                                      >15:21082005-21082035 183_30bp 
##                                                                                                                                                                                                                                    "ttcatggcctttgggttgcttctatctctt" 
##                                                                                                                                                                                                                                     >16:14989693-14989868 116_175bp 
##                                                                                   "TGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCA" 
##                                                                                                                                                                                                                                      >16:17690789-17690800 208_11bp 
##                                                                                                                                                                                                                                                       "tggagctggga" 
##                                                                                                                                                                                                                                      >16:17690802-17690847 210_45bp 
##                                                                                                                                                                                                                     "taaacccagatcttccaaacaacaaattctctgctcatttcaAGA" 
##                                                                                                                                                                                                                                      >16:18089070-18089116 109_46bp 
##                                                                                                                                                                                                                    "agagagggagggaggaaggaaggaaggaaggaaggaaggaaaacct" 
##                                                                                                                                                                                                                                        >17:4550782-4550844 206_62bp 
##                                                                                                                                                                                                    "gggaccaaaaacaaccacctctcacgcgcttactcagtgccagcacccgcgctccgcctttt" 
##                                                                                                                                                                                                                                       >2:95526518-95526601 268_83bp 
##                                                                                                                                                                               "AGAGGCCGCAAAAGCCCGAGGGCTCCAAGAACTGCCTGCAGAGGCTCAGGGACTGCGAGCTGTCCGCGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 252_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                     >3:196196004-196196051 123_47bp 
##                                                                                                                                                                                                                   "CTGGGGGTGGCTCATCTGAACCCTTGGGTGACATCCTTCTGCCCCCA" 
##                                                                                                                                                                                                                                         >4:8288864-8288951 608_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                         >5:865245-865502 1154_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 11895_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                     >5:131945721-131945786 875_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                     >5:131945789-131945799 862_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                     >5:181195621-181195635 113_14bp 
##                                                                                                                                                                                                                                                    "ATCCAGAGAGAGGA" 
##                                                                                                                                                                                                                                     >5:181195639-181195726 116_87bp 
##                                                                                                                                                                           "GCGCGGGTTGGCCGTGTCGGGATCCAAGGTGAGCTCCACTGCAGACAGAGACAGGGAGAAATGTCCCCACGCAGCCAGGCCCCTGGC" 
##                                                                                                                                                                                                                                     >5:181195730-181195744 103_14bp 
##                                                                                                                                                                                                                                                    "TCTTTGCAGGGCCG" 
##                                                                                                                                                                                                                                       >6:30466891-30466928 554_37bp 
##                                                                                                                                                                                                                             "gtggcgcgatctcggctctcggctcactgcggcctcc" 
##                                                                                                                                                                                                                                       >6:62467363-62467402 481_39bp 
##                                                                                                                                                                                                                           "Tggaaggaaggaaggaaggaaggaaggaaggaaggaagg" 
##                                                                                                                                                                                                                                       >6:62467511-62467538 481_27bp 
##                                                                                                                                                                                                                                       "agaaggaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4658_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                      >8:37701095-37701196 243_101bp 
##                                                                                                                                                             "GGGCCGGGGGCGCTTGCTCCCTGCGCAAGGGCCTGGGCGCGCGGGGCCAATGGGACGCTCTGCAAAACCGCCTCCTGCGCCGCTTCCTGGCCGCGCTCCTC" 
##                                                                                                                                                                                                                                       >X:54367258-54367275 718_17bp 
##                                                                                                                                                                                                                                                 "gagaatcgcttgaaccc" 
##                                                                                                                                                                                                                                       >X:54367276-54367320 740_44bp 
##                                                                                                                                                                                                                      "ggaggcggaggttgcagtgagctgagatggcaccgccgcgctcc" 
##                                                                                                                                                                                                                                       >Y:12869910-12869975 675_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool13
##                                                                                                                                                                                                                                       >1:18611255-18611324 187_69bp 
##                                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 183_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                    >10:132135162-132135199 121_37bp 
##                                                                                                                                                                                                                             "GAGCGCGGGCGGGGGCTTCTGGCTCCTGGGGGTTTGT" 
##                                                                                                                                                                                                                                    >2:221871203-221871265 1343_62bp 
##                                                                                                                                                                                                    "caaatacaggagcacccagattcaaaaagcaagttcttacagacattcgaagagacttagac" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 181_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 2343_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                         >5:865245-865502 1563_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                      >5:10649438-10649513 9952_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                     >5:131945721-131945786 637_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                     >5:131945789-131945799 624_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                       >7:37256513-37256545 105_32bp 
##                                                                                                                                                                                                                                  "gagaaggaggaaggaaggaaggaaggaaagaa" 
##                                                                                                                                                                                                                                       >7:37256766-37256788 105_22bp 
##                                                                                                                                                                                                                                            "gggaggaggaagggaagggaga" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 2591_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >9:93435058-93435107 109_49bp 
##                                                                                                                                                                                                                 "gtagaagctcctgaaattttcttttctttccacgctccttttctctctt" 
##                                                                                                                                                                                                                                      >X:82446629-82446671 4642_42bp 
##                                                                                                                                                                                                                        "atgaggaaaaaacagagcaaaagcgcagaaaatttcaaaaac" 
##                                                                                                                                                                                                                                      >X:82446673-82446687 4579_14bp 
##                                                                                                                                                                                                                                                    "gaatacctcttctc" 
##                                                                                                                                                                                                                                       >Y:12869910-12869975 184_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool14
##                                                                                                                                                                                                                                       >1:18611255-18611324 268_69bp 
##                                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 263_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                        >11:1181147-1181217 222_70bp 
##                                                                                                                                                                                            "GGAGCGCGGCGTGGAGTGCACCTACAAAGCTGAGGGTGAGCGGCCGGCAGCCCCTGGGGCTGGGGTCCGG" 
##                                                                                                                                                                                                                                     >16:14989690-14989868 107_178bp 
##                                                                                "AGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCA" 
##                                                                                                                                                                                                                                      >16:48441125-48441181 130_56bp 
##                                                                                                                                                                                                          "TGGTAGAGGGAAGAGCCCAAGTGGGAAGAATATTTCAGAGGGAGGTGCCAAGCCTC" 
##                                                                                                                                                                                                                                      >17:43755387-43755414 154_27bp 
##                                                                                                                                                                                                                                       "GCGCGGGGCCGCGGCTTCCGGCCCTTC" 
##                                                                                                                                                                                                                                       >17:43755415-43755424 154_9bp 
##                                                                                                                                                                                                                                                         "GCGGCCGAG" 
##                                                                                                                                                                                                                                     >2:234950963-234951013 112_50bp 
##                                                                                                                                                                                                                "AGGACCAGGAGCAACAAATGTTGGCTTCTTCCCCGGCAAAGACCCGCGCT" 
##                                                                                                                                                                                                                                      >20:36986623-36986655 824_32bp 
##                                                                                                                                                                                                                                  "gaaatggttctcctgggttgtcttcttttagg" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 776_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288959 1995_95bp 
##                                                                                                                                                                   "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtctctctctct" 
##                                                                                                                                                                                                                                          >5:865245-865502 793_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 10509_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945799 1567_78bp 
##                                                                                                                                                                                    "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCC" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4470_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >Y:12869910-12869975 278_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool15
##                                                                                                                                                                                                                                       >1:18611255-18611336 621_81bp 
##                                                                                                                                                                                 "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307508-6307583 570_75bp 
##                                                                                                                                                                                       "ttttccttccttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                      >10:70183632-70183662 106_30bp 
##                                                                                                                                                                                                                                    "gagaaggaggaaggaaggaaggaaggaaAA" 
##                                                                                                                                                                                                                                    >10:100122122-100122149 144_27bp 
##                                                                                                                                                                                                                                       "agggagggaggaaggaaggaaggaagg" 
##                                                                                                                                                                                                                                    >10:100122170-100122193 140_23bp 
##                                                                                                                                                                                                                                           "aggaaggaaggaaggaaaatttg" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 815_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                         >4:8288864-8288951 309_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                          >5:865245-865502 938_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 11662_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945786 1053_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                    >5:131945789-131945799 1043_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                       >6:62467363-62467402 155_39bp 
##                                                                                                                                                                                                                           "Tggaaggaaggaaggaaggaaggaaggaaggaaggaagg" 
##                                                                                                                                                                                                                                       >6:62467511-62467538 155_27bp 
##                                                                                                                                                                                                                                       "agaaggaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4016_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                     >X:153867168-153867235 102_67bp 
##                                                                                                                                                                                               "GAGAGCCACGAGGACCGAGGGCCAAGGAACAAATGGCTCATTCTGGCACCAAGGGAGTCCAGCCCCC" 
##                                                                                                                                                                                                                                       >Y:12869910-12869975 411_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool16
##                                                                                                                                                                                                                                       >1:11748568-11748616 556_48bp 
##                                                                                                                                                                                                                  "ACATGTACCGGGAGCGCGGGGGTGAGCTCCTGGTCCACACTGGTGAGG" 
##                                                                                                                                                                                                                                       >1:18611255-18611336 726_81bp 
##                                                                                                                                                                                 "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307508-6307583 421_75bp 
##                                                                                                                                                                                       "ttttccttccttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                        >11:1289723-1289777 189_54bp 
##                                                                                                                                                                                                            "gcggcaagaccctgtgcgcccagcggggcggacacatgcatgctctgtccctgg" 
##                                                                                                                                                                                                                                     >16:14989690-14989869 180_179bp 
##                                                                               "AGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAG" 
##                                                                                                                                                                                                                                        >17:4550782-4550844 300_62bp 
##                                                                                                                                                                                                    "gggaccaaaaacaaccacctctcacgcgcttactcagtgccagcacccgcgctccgcctttt" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 576_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 3404_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                         >5:865245-865502 2419_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                      >5:10649438-10649513 9805_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945799 1392_78bp 
##                                                                                                                                                                                    "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCC" 
##                                                                                                                                                                                                                                         >8:1974504-1974546 708_42bp 
##                                                                                                                                                                                                                        "CCCTGGGGAGGGGAGCGCGGCCCTTGGTCCTCCGCCGCTGCG" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 3942_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >8:41063496-41063528 217_32bp 
##                                                                                                                                                                                                                                  "agggaaggagggaaggaggaaggaaggaaAAT" 
##                                                                                                                                                                                                                                         >X:2213846-2213880 141_34bp 
##                                                                                                                                                                                                                                "agggaaggaggaaggaaggaggaaggaagggaag" 
##                                                                                                                                                                                                                                         >X:2214118-2214156 144_38bp 
##                                                                                                                                                                                                                            "aggaaggaagggaaggaggaaggaaggaggaaggaagg" 
##                                                                                                                                                                                                                                         >X:3983551-3983596 328_45bp 
##                                                                                                                                                                                                                     "aggaaagagggagggagggaggaaggaaggaaggaaggaaaATTT" 
##                                                                                                                                                                                                                                       >Y:12869918-12869975 319_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool17
##                                                                                                                                                                                                                     >4:8288864-8288951 3435_87bp 
##                                                                                                                                                        "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                       >5:865252-865490 133_238bp 
## "GCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCC" 
##                                                                                                                                                                                                                  >5:10649438-10649513 12054_75bp 
##                                                                                                                                                                    "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                  >5:131945721-131945786 510_65bp 
##                                                                                                                                                                              "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                  >5:131945789-131945799 504_10bp 
##                                                                                                                                                                                                                                     "CGCAGGTTCC" 
##                                                                                                                                                                                                                  >8:22055623-22055743 1924_120bp 
##                                                                                                                       "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
## 
## $pool18
##                                                                                                                                                                                                                                                                                   >1:18611255-18611336 335_81bp 
##                                                                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                                                                    >10:6307522-6307583 121_61bp 
##                                                                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                                                                >10:131347243-131347276 103_33bp 
##                                                                                                                                                                                                                                                                             "ttccttccttccttcctccttctctcattcttt" 
##                                                                                                                                                                                                                                                                                  >16:14989617-14989628 150_11bp 
##                                                                                                                                                                                                                                                                                                   "GGACCCCGCGG" 
##                                                                                                                                                                                                                                                                                 >16:14989629-14989930 302_301bp 
## "AAGGCCAGAGACGGAggcgggcccggggccggcggccacggggccAGGACCTGGGGACCCCAGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAGGAAGCCGTTGGCCACCAGGGCCGGCACTCCAGGGCCCAGCGGTACCGCCTCGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                 >22:29788944-29789092 197_148bp 
##                                                                                                                                                          "CCCAGGCGATGGGAGCACGGCCTGGTGAGTCTGGTGCCGCTGCCTCCCCACTGGCCCTGCACCAGGTCTCAGGATGGGATCATGCCTTTGCTCCTCTTGCGGTCGGCCATGGTTCTCCGGTTGTGGTTGGCTCTTGTCGCCTTGTTGG" 
##                                                                                                                                                                                                                                                                                  >22:29789093-29789115 197_22bp 
##                                                                                                                                                                                                                                                                                        "TTCCTTCTTCCTGCGTTCCTGG" 
##                                                                                                                                                                                                                                                                                  >22:29789117-29789132 196_15bp 
##                                                                                                                                                                                                                                                                                               "TGTCTCGCGGCTCTG" 
##                                                                                                                                                                                                                                                                                  >22:46679451-46679485 185_34bp 
##                                                                                                                                                                                                                                                                            "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                                                                    >4:8288864-8288951 1958_87bp 
##                                                                                                                                                                                                                       "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                                                                   >4:31367013-31367064 316_51bp 
##                                                                                                                                                                                                                                                           "AGATGAAGGAGGAAGGATTTTGAAGTCCCCTGTGGAAAATCTgggaataag" 
##                                                                                                                                                                                                                                                                                     >5:865245-865502 2675_257bp 
##                                             "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                                                                  >5:10649438-10649513 6016_75bp 
##                                                                                                                                                                                                                                   "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                 >5:131945721-131945786 536_65bp 
##                                                                                                                                                                                                                                             "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                                                                 >5:131945789-131945799 526_10bp 
##                                                                                                                                                                                                                                                                                                    "CGCAGGTTCC" 
##                                                                                                                                                                                                                                                                                 >8:22055623-22055743 2302_120bp 
##                                                                                                                                                                                      "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                                                                   >Y:12869910-12869975 127_65bp 
##                                                                                                                                                                                                                                             "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool19
##                                                                                                                                                                                                                                    >11:115173455-115173532 313_77bp 
##                                                                                                                                                                                     "AGAAGGAGAGAGAGCGCGGCCCCCAGCAACCCAGCCGGCAGCATGTCCTAGCATCTACTGCCAGCGTTCCTGGCCCC" 
##                                                                                                                                                                                                                                     >12:132583203-132583212 344_9bp 
##                                                                                                                                                                                                                                                         "TGAAGGTCA" 
##                                                                                                                                                                                                                                    >12:132583214-132583258 345_44bp 
##                                                                                                                                                                                                                      "GAGGAGCGCGGGGAGGACGAGGCCTCCGAGCCCCCGGCGGGCGG" 
##                                                                                                                                                                                                                                      >13:69077731-69077797 210_66bp 
##                                                                                                                                                                                                "AACCCAAGAAACAACATTGTTTTTTACAAAAATAACAATCAACTAATATACATAAAATTTCAAGAA" 
##                                                                                                                                                                                                                                     >16:14989689-14989870 197_181bp 
##                                                                             "CAGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAGG" 
##                                                                                                                                                                                                                                      >16:66767740-66767838 201_98bp 
##                                                                                                                                                                "tttttgagatggagtctcactctgtcgtccaggctggagtgcagtggcatgatctcggctcactgcaacctccgcctcctgggttgaagcagttctcc" 
##                                                                                                                                                                                                                                        >17:4550782-4550844 138_62bp 
##                                                                                                                                                                                                    "gggaccaaaaacaaccacctctcacgcgcttactcagtgccagcacccgcgctccgcctttt" 
##                                                                                                                                                                                                                                       >2:95526518-95526601 111_83bp 
##                                                                                                                                                                               "AGAGGCCGCAAAAGCCCGAGGGCTCCAAGAACTGCCTGCAGAGGCTCAGGGACTGCGAGCTGTCCGCGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 443_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288955 4024_91bp 
##                                                                                                                                                                       "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtctctct" 
##                                                                                                                                                                                                                                         >5:865245-865502 3139_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 11258_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945786 1376_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                    >5:131945789-131945799 1358_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4129_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
## 
## $pool2
##                                                                                                                                                                                                                                       >1:18611255-18611336 555_81bp 
##                                                                                                                                                                                 "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 399_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                    >10:100122122-100122193 203_71bp 
##                                                                                                                                                                                           "agggagggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaaatttg" 
##                                                                                                                                                                                                                                       >12:7913634-7913754 229_120bp 
##                                                                                                                                          "CACGGCAAAATGtttattttatttttgatacagagtttcgctcttgttgcccaggctggagtgtaatggcactatcttggctcaccgtaacctctgcctcctgggttcaagcgattctcc" 
##                                                                                                                                                                                                                                      >17:81103010-81103061 310_51bp 
##                                                                                                                                                                                                               "GGAGCGCGGGCTCTTGGGCCCAAGGGCAGTGGTTGGAGCAGTGAGCCTCAG" 
##                                                                                                                                                                                                                                      >17:81103064-81103080 298_16bp 
##                                                                                                                                                                                                                                                  "GTCTGACGGGGCTGCC" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 818_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                       >3:14555195-14555262 136_67bp 
##                                                                                                                                                                                               "GCCCAGAGCCAGGCAGCCTTCACCTATGTccccctgtcccaactccccacgtacagcccctcgctcc" 
##                                                                                                                                                                                                                                         >4:8288864-8288951 418_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                         >5:865245-865502 1057_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 12873_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945799 2815_78bp 
##                                                                                                                                                                                    "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCC" 
##                                                                                                                                                                                                                                       >6:96925095-96925147 121_52bp 
##                                                                                                                                                                                                              "CCAAGTGGGGGCAGACCCGGAGTTGACATTTCAGGGGCTTGCAGCCCATGCA" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4618_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                     >9:129284217-129284230 523_13bp 
##                                                                                                                                                                                                                                                     "gggaacgggtggc" 
##                                                                                                                                                                                                                                     >9:129284232-129284318 533_86bp 
##                                                                                                                                                                            "aacccagacctgcccagtttcaTGTTCGCGCCGTGAGGGGTCCAGCGGCTGTGGTGTCACTTCTGGTTACCCCGTCATTTAGAGGG" 
##                                                                                                                                                                                                                                       >X:32216848-32216897 595_49bp 
##                                                                                                                                                                                                                 "AAGAAGTTAAAGAGTCCAGATGTGCTGAAGATAAATACAATTTCGAAAA" 
##                                                                                                                                                                                                                                       >Y:12869905-12869975 508_70bp 
##                                                                                                                                                                                            "Tttccttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool20
##                                                                                                                                                                                                                                                                                 >10:10027960-10028013 1258_53bp 
##                                                                                                                                                                                                                                                         "cagaaatagaggggcccaagcaagggattgcaactcaatttcaaaaacttctg" 
##                                                                                                                                                                                                                                                                                  >16:14989617-14989628 110_11bp 
##                                                                                                                                                                                                                                                                                                   "GGACCCCGCGG" 
##                                                                                                                                                                                                                                                                                 >16:14989629-14989930 224_301bp 
## "AAGGCCAGAGACGGAggcgggcccggggccggcggccacggggccAGGACCTGGGGACCCCAGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAGGAAGCCGTTGGCCACCAGGGCCGGCACTCCAGGGCCCAGCGGTACCGCCTCGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                  >21:39108618-39108702 123_84bp 
##                                                                                                                                                                                                                          "CAAGGCCCGGGCTCCAGGGGCCCTAACCAGGTGTGGGCTGAGAACGGGAGCTCCCCAAGGGCGGGCCGCGCTCCTCATCCTCTC" 
##                                                                                                                                                                                                                                                                                  >22:46679451-46679485 229_34bp 
##                                                                                                                                                                                                                                                                            "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                                                                   >4:8288864-8288967 1632_103bp 
##                                                                                                                                                                                                       "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtctctctctcttttttttt" 
##                                                                                                                                                                                                                                                                                     >5:865245-865502 1593_257bp 
##                                             "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                                                                  >5:10649438-10649513 4777_75bp 
##                                                                                                                                                                                                                                   "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                 >5:131945721-131945786 143_65bp 
##                                                                                                                                                                                                                                             "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                                                                 >5:131945789-131945799 141_10bp 
##                                                                                                                                                                                                                                                                                                    "CGCAGGTTCC" 
##                                                                                                                                                                                                                                                                                 >8:22055623-22055743 2318_120bp 
##                                                                                                                                                                                      "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
## 
## $pool21
##                                                                                                                                                                                                                                       >1:18611255-18611324 356_69bp 
##                                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 400_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                      >10:80473306-80473343 487_37bp 
##                                                                                                                                                                                                                             "TCCTGAAACTTGGCAGGTTTTGGGTTGTGAGTTTTTG" 
##                                                                                                                                                                                                                                    >10:132135162-132135199 164_37bp 
##                                                                                                                                                                                                                             "GAGCGCGGGCGGGGGCTTCTGGCTCCTGGGGGTTTGT" 
##                                                                                                                                                                                                                                    >12:105330765-105330791 229_26bp 
##                                                                                                                                                                                                                                        "TCGGTTCCTGGCCCCTCGCGGCCCCG" 
##                                                                                                                                                                                                                                     >16:14989690-14989869 171_179bp 
##                                                                               "AGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAG" 
##                                                                                                                                                                                                                                       >20:37944304-37944312 125_8bp 
##                                                                                                                                                                                                                                                          "AGGAGCCG" 
##                                                                                                                                                                                                                                      >20:37944313-37944351 128_38bp 
##                                                                                                                                                                                                                            "CGGACCACCGGGGACCGACTGCCTGCGTCCAGCCGCGC" 
##                                                                                                                                                                                                                                     >22:43974366-43974508 202_142bp 
##                                                                                                                    "tgaaggacaggagcgcggggtctcccagggccgttgtgagggttggatgagaggcgtggtaaagctcctgatgcggcgcgtggcgcagtttaggtgcttgaGGTGCGTTAGTGCCCCAGGCCTCTGGTCCTTGCAGACCAAG" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 130_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 3145_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                         >5:865245-865502 2678_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 10108_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945800 4480_79bp 
##                                                                                                                                                                                   "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCCT" 
##                                                                                                                                                                                                                                     >5:132200546-132200578 120_32bp 
##                                                                                                                                                                                                                                  "cttttttttGGGGGGAGTGGGGGtagagacag" 
##                                                                                                                                                                                                                                       >7:63398175-63398190 101_15bp 
##                                                                                                                                                                                                                                                   "GGAGCGCGGGAGGTC" 
##                                                                                                                                                                                                                                       >7:63398191-63398273 101_82bp 
##                                                                                                                                                                                "TAGCTGCAGCCGGACGAGCGCTGGCACCAGCCGGGCACCGCGCATGGATCCCGCGTGCGCACTGTCGCGGTCATGGCGTCCC" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4281_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                     >X:153420796-153420848 102_52bp 
##                                                                                                                                                                                                              "GGGGCCGCAGGGCCCCAAAGGCGCGGAGAAGCGGTACCTGTGCCAGCagtgt" 
##                                                                                                                                                                                                                                    >X:153420849-153420964 102_115bp 
##                                                                                                                                               "ggaaggccttcagccgcagctccaacctcatcaagcaccgcatcatccacagtggcgagaagccttacgcgtgccccgagtgcggcaagctgtttcgccgcagcttcgcgctcct" 
##                                                                                                                                                                                                                                       >Y:12869910-12869975 354_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool22
##                                                                                                                                                                                                                                       >1:18611255-18611340 317_85bp 
##                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                     >1:112387835-112387898 292_63bp 
##                                                                                                                                                                                                   "agagagagaggaaggaaggaaggaaggaaggaaggaaggaaggaagggagggaaggaaggaga" 
##                                                                                                                                                                                                                                     >1:112387982-112388053 292_71bp 
##                                                                                                                                                                                           "aggaagggagggagggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaaa" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 179_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                    >10:131346939-131346970 375_31bp 
##                                                                                                                                                                                                                                   "ccttccctccttccttccttcctccctccct" 
##                                                                                                                                                                                                                                    >10:131346990-131347017 272_27bp 
##                                                                                                                                                                                                                                       "ctctccttccttcctccctccctccct" 
##                                                                                                                                                                                                                                    >10:131347240-131347276 648_36bp 
##                                                                                                                                                                                                                              "tccttccttccttccttcctccttctctcattcttt" 
##                                                                                                                                                                                                                                    >11:113627262-113627297 146_35bp 
##                                                                                                                                                                                                                               "agggagggaggaaggaaggaagggagggagggagg" 
##                                                                                                                                                                                                                                    >11:113627447-113627478 145_31bp 
##                                                                                                                                                                                                                                   "aaggaggaaggaaggaaggaaggaaggaaaa" 
##                                                                                                                                                                                                                                      >13:27351867-27351917 127_50bp 
##                                                                                                                                                                                                                "cccaggctagagtgcagtggcataaccacaactcattgaactcatttcag" 
##                                                                                                                                                                                                                                        >21:8205418-8205474 107_56bp 
##                                                                                                                                                                                                          "CGTGGCGCGGGAGGCTGGGGACGCCCTTCCCGGCCCGGTCGCGGGTCCGCGCTCAT" 
##                                                                                                                                                                                                                                        >21:8205475-8205485 104_10bp 
##                                                                                                                                                                                                                                                        "CTGGCCGTCT" 
##                                                                                                                                                                                                                                        >21:8249608-8249664 111_56bp 
##                                                                                                                                                                                                          "CGTGGCGCGGGAGGCTGGGGACGCCCTTCCCGGCCCGGTCGCGGGTCCGCGCTCAT" 
##                                                                                                                                                                                                                                        >21:8249665-8249675 111_10bp 
##                                                                                                                                                                                                                                                        "CTGGCCGTCT" 
##                                                                                                                                                                                                                                        >21:8388465-8388521 110_56bp 
##                                                                                                                                                                                                          "CGTGGCGCGGGAGGCTGGGGACGCCCTTCCCGGCCCGGTCGCGGGTCCGCGCTCAT" 
##                                                                                                                                                                                                                                        >21:8388522-8388532 109_10bp 
##                                                                                                                                                                                                                                                        "CTGGCCGTCT" 
##                                                                                                                                                                                                                                        >21:8432633-8432687 102_54bp 
##                                                                                                                                                                                                            "CGTGGCGCGGGAGGCTGGGGACGCCCTTCCCGGCCCGGTCGCGGGTCCGCGCTC" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 380_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                         >5:865245-865502 1692_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 13348_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945799 1965_78bp 
##                                                                                                                                                                                    "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCC" 
##                                                                                                                                                                                                                                       >7:37256513-37256561 126_48bp 
##                                                                                                                                                                                                                  "gagaaggaggaaggaaggaaggaaggaaagaaggaagaaaggaaggaa" 
##                                                                                                                                                                                                                                       >7:37256753-37256804 123_51bp 
##                                                                                                                                                                                                               "agggaagggagaagggaggaggaagggaagggagaagggagggagggaaag" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 4642_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                  >GL000220.1:104835-104891 107_56bp 
##                                                                                                                                                                                                          "CGTGGCGCGGGAGGCTGGGGACGCCCTTCCCGGCCCGGTCGCGGGTCCGCGCTCAT" 
##                                                                                                                                                                                                                                  >GL000220.1:104892-104902 106_10bp 
##                                                                                                                                                                                                                                                        "CTGGCCGTCT" 
##                                                                                                                                                                                                                                  >KI270733.1:121684-121740 113_56bp 
##                                                                                                                                                                                                          "CGTGGCGCGGGAGGCTGGGGACGCCCTTCCCGGCCCGGTCGCGGGTCCGCGCTCAT" 
##                                                                                                                                                                                                                                  >KI270733.1:121741-121751 112_10bp 
##                                                                                                                                                                                                                                                        "CTGGCCGTCT" 
##                                                                                                                                                                                                                                  >KI270733.1:166771-166804 100_33bp 
##                                                                                                                                                                                                                                 "CGCGGGAGGCTGGGGACGCCCTTCCCGGCCCGG" 
##                                                                                                                                                                                                                                       >Y:12869925-12869974 102_49bp 
##                                                                                                                                                                                                                 "cttccttccttccttccttccttccttccttccttcctccttctctccc" 
## 
## $pool23
##                                                                                                                                                                                                                                       >1:18611255-18611344 564_89bp 
##                                                                                                                                                                         "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307512-6307583 246_71bp 
##                                                                                                                                                                                           "ccttccttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                      >10:70005108-70005147 117_39bp 
##                                                                                                                                                                                                                           "agggaaggggaggggaggggaggaagggaaaagggaaaa" 
##                                                                                                                                                                                                                                      >10:70005357-70005404 117_47bp 
##                                                                                                                                                                                                                   "agggagggagggagggaggaaggaaggaaggaaggaaggaaggaaaa" 
##                                                                                                                                                                                                                                    >10:131346939-131346970 238_31bp 
##                                                                                                                                                                                                                                   "ccttccctccttccttccttcctccctccct" 
##                                                                                                                                                                                                                                    >10:131346990-131347017 318_27bp 
##                                                                                                                                                                                                                                       "ctctccttccttcctccctccctccct" 
##                                                                                                                                                                                                                                    >10:131347240-131347276 554_36bp 
##                                                                                                                                                                                                                              "tccttccttccttccttcctccttctctcattcttt" 
##                                                                                                                                                                                                                                     >11:80568673-80568788 280_115bp 
##                                                                                                                                               "GCTCCTGAAACAATGAGGTAGCCCAGTGTGTGTTTGTGTGTATGCGTGTGGCTCAGTACTTCACACCTGAGAGGTATGAGTGTTCACTACAAAGAGGAACTggaaagctttgggc" 
##                                                                                                                                                                                                                                      >11:80568796-80568810 275_14bp 
##                                                                                                                                                                                                                                                    "catgttcactctct" 
##                                                                                                                                                                                                                                     >16:14989694-14989865 108_171bp 
##                                                                                       "GCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGG" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 400_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                         >4:8288864-8288929 125_65bp 
##                                                                                                                                                                                                 "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttc" 
##                                                                                                                                                                                                                                         >5:865245-865502 1566_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                      >5:10649438-10649513 8843_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945786 1012_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                    >5:131945789-131945799 1003_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                       >7:37256513-37256549 206_36bp 
##                                                                                                                                                                                                                              "gagaaggaggaaggaaggaaggaaggaaagaaggaa" 
##                                                                                                                                                                                                                                       >7:37256753-37256803 202_50bp 
##                                                                                                                                                                                                                "agggaagggagaagggaggaggaagggaagggagaagggagggagggaaa" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 1943_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                  >KI270733.1:133694-133777 106_83bp 
##                                                                                                                                                                               "cgcggcggcggcggcggcggcgggcggcggaggggccgcgggccggtcccccccgccgggtccgcccccggggccgcggttcc" 
##                                                                                                                                                                                                                                  >KI270733.1:178774-178856 105_82bp 
##                                                                                                                                                                                "gcggcggcggcggcggcggcgggcggcggaggggccgcgggccggtcccccccgccgggtccgcccccggggccgcggttcc" 
##                                                                                                                                                                                                                                       >Y:12869910-12869975 183_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool24
##                                                                                                                                                                                                                                                                                  >1:43926216-43926323 356_107bp 
##                                                                                                                                                                                                   "acagagagtgagaagCGCGGCTCATCCTGGCAGGACCCTTGAACGTGGATACTTAACGGTTGGGCGAGGAGCCAAAGAAAAAGAGCTTCTggccgggcgcggtccct" 
##                                                                                                                                                                                                                                                                                  >11:78417513-78417543 330_30bp 
##                                                                                                                                                                                                                                                                                "gctcctcgcccccggccccccgcggctccg" 
##                                                                                                                                                                                                                                                                                >12:105330765-105330791 503_26bp 
##                                                                                                                                                                                                                                                                                    "TCGGTTCCTGGCCCCTCGCGGCCCCG" 
##                                                                                                                                                                                                                                                                                  >16:14989617-14989628 109_11bp 
##                                                                                                                                                                                                                                                                                                   "GGACCCCGCGG" 
##                                                                                                                                                                                                                                                                                 >16:14989629-14989930 219_301bp 
## "AAGGCCAGAGACGGAggcgggcccggggccggcggccacggggccAGGACCTGGGGACCCCAGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAGGAAGCCGTTGGCCACCAGGGCCGGCACTCCAGGGCCCAGCGGTACCGCCTCGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                    >17:4550782-4550844 390_62bp 
##                                                                                                                                                                                                                                                "gggaccaaaaacaaccacctctcacgcgcttactcagtgccagcacccgcgctccgcctttt" 
##                                                                                                                                                                                                                                                                                 >19:11551551-11551692 224_141bp 
##                                                                                                                                                                 "CAGAGAAGCGAGGAGCGCGGCACGGAGCTGTCTTCTCCCCAGGGAGGGCAGGAGTTGAGGCTGGAACGTGGAGACCTGCGGAGGCAGACACCAGAAGACCCGCGCACAGACGCACGCAGCCCCTGGGGCCTCGTAAACCGG" 
##                                                                                                                                                                                                                                                                                  >19:38326060-38326071 119_11bp 
##                                                                                                                                                                                                                                                                                                   "tcactgacaga" 
##                                                                                                                                                                                                                                                                                  >19:38326072-38326126 119_54bp 
##                                                                                                                                                                                                                                                        "ggagtgcggcatgagtgacgagggcgtcagggatgaaggcaaggctcttggcct" 
##                                                                                                                                                                                                                                                                                  >22:46679451-46679485 259_34bp 
##                                                                                                                                                                                                                                                                            "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                                                                    >4:8288864-8288951 1128_87bp 
##                                                                                                                                                                                                                       "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                                                                     >5:865245-865502 2330_257bp 
##                                             "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                                                                  >5:10649438-10649513 7273_75bp 
##                                                                                                                                                                                                                                   "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                >5:131945721-131945786 1272_65bp 
##                                                                                                                                                                                                                                             "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                                                                >5:131945789-131945799 1251_10bp 
##                                                                                                                                                                                                                                                                                                    "CGCAGGTTCC" 
##                                                                                                                                                                                                                                                                                     >8:1974504-1974546 185_42bp 
##                                                                                                                                                                                                                                                                    "CCCTGGGGAGGGGAGCGCGGCCCTTGGTCCTCCGCCGCTGCG" 
##                                                                                                                                                                                                                                                                                  >8:22055623-22055726 870_103bp 
##                                                                                                                                                                                                       "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCT" 
##                                                                                                                                                                                                                                                                                   >8:22055727-22055743 862_16bp 
##                                                                                                                                                                                                                                                                                              "CCTTCTCTCTGGAGCC" 
## 
## $pool3
##                                                                                                                                                                                                                                       >1:18611255-18611336 529_81bp 
##                                                                                                                                                                                 "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307526-6307583 419_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                      >16:15177391-15177437 110_46bp 
##                                                                                                                                                                                                                    "agagagggagggaggaaggaaggaaggaaggaaggaaggaaaacct" 
##                                                                                                                                                                                                                                        >17:4550782-4550844 150_62bp 
##                                                                                                                                                                                                    "gggaccaaaaacaaccacctctcacgcgcttactcagtgccagcacccgcgctccgcctttt" 
##                                                                                                                                                                                                                                      >17:62060954-62061019 288_65bp 
##                                                                                                                                                                                                 "cccaaaagtgctgggattacaggcgtgagtgagccatggcacccagcTGATCACTATTTTAAAGG" 
##                                                                                                                                                                                                                                      >17:65561479-65561525 948_46bp 
##                                                                                                                                                                                                                    "cggccgccgggcggccccgAAATCCATCGCTCTGAGGGGTTATTTT" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 482_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                         >4:8288865-8288898 112_33bp 
##                                                                                                                                                                                                                                 "cCACCCCCAAATTttccttccttccttccgtcc" 
##                                                                                                                                                                                                                                          >5:865245-865502 834_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 16465_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945786 1525_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                    >5:131945789-131945799 1495_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 2893_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                      >8:144560678-144560685 111_7bp 
##                                                                                                                                                                                                                                                           "tcgagga" 
##                                                                                                                                                                                                                                     >8:144560686-144560738 111_52bp 
##                                                                                                                                                                                                              "cagcggtgcgcgggttactctgttactgagttagatgaatatcatgttcctg" 
##                                                                                                                                                                                                                                     >X:119552588-119552625 136_37bp 
##                                                                                                                                                                                                                             "cagaagcctcccaaaccctgtcctcctgggttgttat" 
##                                                                                                                                                                                                                                      >X:119552627-119552635 136_8bp 
##                                                                                                                                                                                                                                                          "aagctttg" 
##                                                                                                                                                                                                                                       >Y:12869918-12869975 288_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool4
##                                                                                                                                                                                                                                                                                   >1:18611255-18611336 315_81bp 
##                                                                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                                                                    >10:6307508-6307583 230_75bp 
##                                                                                                                                                                                                                                   "ttttccttccttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                                                                >10:103584482-103584577 117_95bp 
##                                                                                                                                                                                                               "cggggccgccTCCCGAGAGCCCTGCGTGACACTGCCCCGTGTCTCCCGCGCAGATAGCGAGCTGGTGCTCCCGGACTGTCTGCGGCCGCGCTCCT" 
##                                                                                                                                                                                                                                                                                  >16:14989617-14989628 107_11bp 
##                                                                                                                                                                                                                                                                                                   "GGACCCCGCGG" 
##                                                                                                                                                                                                                                                                                 >16:14989629-14989930 213_301bp 
## "AAGGCCAGAGACGGAggcgggcccggggccggcggccacggggccAGGACCTGGGGACCCCAGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCAGGAAGCCGTTGGCCACCAGGGCCGGCACTCCAGGGCCCAGCGGTACCGCCTCGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                  >22:46679451-46679485 238_34bp 
##                                                                                                                                                                                                                                                                            "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                                                                     >4:3611860-3611931 106_71bp 
##                                                                                                                                                                                                                                       "GGAGCGCGGAGAGCAAGGCTGGGCAGAGAGGCATCTTCTCAGGGTGCCTCGCCCTGGGGGCCCAGCGGCAG" 
##                                                                                                                                                                                                                                                                                    >4:8288864-8288951 2350_87bp 
##                                                                                                                                                                                                                       "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                                                                     >5:865245-865502 1249_257bp 
##                                             "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                                                                 >5:10649438-10649513 11784_75bp 
##                                                                                                                                                                                                                                   "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                                                                   >5:66573511-66573558 130_47bp 
##                                                                                                                                                                                                                                                               "agggagggagggagggaggaaggaaggaaggaaAAtttaggaacaag" 
##                                                                                                                                                                                                                                                                                >5:131945721-131945800 2391_79bp 
##                                                                                                                                                                                                                               "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCCT" 
##                                                                                                                                                                                                                                                                                 >6:104424412-104424455 127_43bp 
##                                                                                                                                                                                                                                                                   "aggaagggagggaggaaggaaggaaggaaAATTTTTTCCCAGT" 
##                                                                                                                                                                                                                                                                                 >8:22055623-22055743 3973_120bp 
##                                                                                                                                                                                      "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
## 
## $pool5
##                                                                                                                                                                                                                                       >1:18611255-18611340 239_85bp 
##                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                     >1:112387835-112387898 195_63bp 
##                                                                                                                                                                                                   "agagagagaggaaggaaggaaggaaggaaggaaggaaggaaggaagggagggaaggaaggaga" 
##                                                                                                                                                                                                                                     >1:112387982-112388053 195_71bp 
##                                                                                                                                                                                           "aggaagggagggagggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaaa" 
##                                                                                                                                                                                                                                    >10:131346939-131346970 195_31bp 
##                                                                                                                                                                                                                                   "ccttccctccttccttccttcctccctccct" 
##                                                                                                                                                                                                                                    >10:131346990-131347017 236_27bp 
##                                                                                                                                                                                                                                       "ctctccttccttcctccctccctccct" 
##                                                                                                                                                                                                                                    >10:131347240-131347276 424_36bp 
##                                                                                                                                                                                                                              "tccttccttccttccttcctccttctctcattcttt" 
##                                                                                                                                                                                                                                    >11:113627262-113627297 190_35bp 
##                                                                                                                                                                                                                               "agggagggaggaaggaaggaagggagggagggagg" 
##                                                                                                                                                                                                                                    >11:113627447-113627478 187_31bp 
##                                                                                                                                                                                                                                   "aaggaggaaggaaggaaggaaggaaggaaaa" 
##                                                                                                                                                                                                                                      >15:76814085-76814137 174_52bp 
##                                                                                                                                                                                                              "tgaacccgggaggcagaggctgctgtgagccgagattacgccaccgcgctcc" 
##                                                                                                                                                                                                                                        >18:3412110-3412182 212_72bp 
##                                                                                                                                                                                          "GAGGGCCGCAGGGAGCCAGAGACTCGAGCCTgcggttccagccccgccgcggttccggccccgccgcgATCC" 
##                                                                                                                                                                                                                                      >18:80001920-80001951 100_31bp 
##                                                                                                                                                                                                                                   "gcttttgaaatatgaggacatgagatttggg" 
##                                                                                                                                                                                                                                      >21:28059665-28059710 108_45bp 
##                                                                                                                                                                                                                     "gggaaggcatgattgtttttgaaatgtgaggatatgagatttggg" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 241_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                          >5:865245-865502 901_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 13490_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                       >5:21485325-21485356 102_31bp 
##                                                                                                                                                                                                                                   "cccaaatctcatgtcctcatatttcaaaagc" 
##                                                                                                                                                                                                                                       >5:34188811-34188842 105_31bp 
##                                                                                                                                                                                                                                   "gcttttgaaatatgaggacatgagatttggg" 
##                                                                                                                                                                                                                                       >5:69652010-69652055 104_45bp 
##                                                                                                                                                                                                                     "gggaaggcacgattgcttttgaaatatgaggacatgagatttggg" 
##                                                                                                                                                                                                                                       >5:69904397-69904442 101_45bp 
##                                                                                                                                                                                                                     "cccaaatctcatgtcctcatatttcaaaagcaatcatgccttccc" 
##                                                                                                                                                                                                                                       >5:70213701-70213746 106_45bp 
##                                                                                                                                                                                                                     "gggaaggcacgattgcttttgaaatatgaggacatgagatttggg" 
##                                                                                                                                                                                                                                       >5:70528127-70528172 109_45bp 
##                                                                                                                                                                                                                     "gggaaggcatgattgcttttgaaatatgaggacatgagatttggg" 
##                                                                                                                                                                                                                                       >5:71232086-71232131 111_45bp 
##                                                                                                                                                                                                                     "gggaaggcatgattgcttttgaaatatgaggacatgagatttggg" 
##                                                                                                                                                                                                                                    >5:131945721-131945799 2036_78bp 
##                                                                                                                                                                                    "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCC" 
##                                                                                                                                                                                                                                     >6:124862224-124862255 100_31bp 
##                                                                                                                                                                                                                                   "cccaaatctcatgtcctcatatttcaaaaac" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 2879_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >X:13044583-13044596 458_13bp 
##                                                                                                                                                                                                                                                     "TGGCACCGCGAAG" 
##                                                                                                                                                                                                                                       >X:13044599-13044672 465_73bp 
##                                                                                                                                                                                         "CTCCGAGGGCCTGGGTCCTCTGTTCTCACGAGAGCAGCAGCCGCCCCGGCTGCCCGCGCTCCTCGCTGATTGG" 
##                                                                                                                                                                                                                                       >Y:12869916-12869975 108_59bp 
##                                                                                                                                                                                                       "ccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool6
##                                                                                                                                                                                                                                       >1:18611255-18611340 612_85bp 
##                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 297_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                    >10:132135162-132135199 150_37bp 
##                                                                                                                                                                                                                             "GAGCGCGGGCGGGGGCTTCTGGCTCCTGGGGGTTTGT" 
##                                                                                                                                                                                                                                      >12:12058886-12058925 267_39bp 
##                                                                                                                                                                                                                           "cagaccaagcagcccaagaaacatctcaccaatttcaaa" 
##                                                                                                                                                                                                                                        >17:4550782-4550844 147_62bp 
##                                                                                                                                                                                                    "gggaccaaaaacaaccacctctcacgcgcttactcagtgccagcacccgcgctccgcctttt" 
##                                                                                                                                                                                                                                      >18:58646198-58646240 342_42bp 
##                                                                                                                                                                                                                        "tttgaaattggtgagatgttctttgggctgtttggtctgagg" 
##                                                                                                                                                                                                                                      >19:28435207-28435249 283_42bp 
##                                                                                                                                                                                                                        "tttgaaattggtgagatgtttcttgggctgcttggtctgagg" 
##                                                                                                                                                                                                                                          >20:897327-897368 345_41bp 
##                                                                                                                                                                                                                         "ctcagatcaaacagcccaaggaacatctcaccaatttcaaa" 
##                                                                                                                                                                                                                                     >20:29876340-29876455 143_115bp 
##                                                                                                                                               "cagcggaaagagcagcgcggcgactggtggtgcttgggcgtagagggggagagcagtccggccaggggaaagtggctctagggtgcctgatcccagccttgtggccccgggtttt" 
##                                                                                                                                                                                                                                     >22:29788944-29789092 139_148bp 
##                                                                                                              "CCCAGGCGATGGGAGCACGGCCTGGTGAGTCTGGTGCCGCTGCCTCCCCACTGGCCCTGCACCAGGTCTCAGGATGGGATCATGCCTTTGCTCCTCTTGCGGTCGGCCATGGTTCTCCGGTTGTGGTTGGCTCTTGTCGCCTTGTTGG" 
##                                                                                                                                                                                                                                      >22:29789093-29789115 136_22bp 
##                                                                                                                                                                                                                                            "TTCCTTCTTCCTGCGTTCCTGG" 
##                                                                                                                                                                                                                                      >22:29789117-29789131 133_14bp 
##                                                                                                                                                                                                                                                    "TGTCTCGCGGCTCT" 
##                                                                                                                                                                                                                                     >22:46679451-46679485 1507_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                       >3:72680749-72680784 100_35bp 
##                                                                                                                                                                                                                               "gaaccagagactgaggacagacaggcccagccccc" 
##                                                                                                                                                                                                                                     >3:179525820-179525862 385_42bp 
##                                                                                                                                                                                                                        "tttgaaattggtgagatgttccttgggttgtttggtctgacg" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 5299_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                         >5:865245-865502 1982_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 18147_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945799 2085_78bp 
##                                                                                                                                                                                    "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTGGCGCAGGTTCC" 
##                                                                                                                                                                                                                                       >7:30480049-30480091 261_42bp 
##                                                                                                                                                                                                                        "cctcagaccaaacagcccaaggaacatctcaccaatttcaaa" 
##                                                                                                                                                                                                                                     >7:143105600-143105642 330_42bp 
##                                                                                                                                                                                                                        "cctcagaccaagcagcccaaggaacatctcaccaatttcaaa" 
##                                                                                                                                                                                                                                         >8:1974504-1974546 215_42bp 
##                                                                                                                                                                                                                        "CCCTGGGGAGGGGAGCGCGGCCCTTGGTCCTCCGCCGCTGCG" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 5609_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >8:41063496-41063528 184_32bp 
##                                                                                                                                                                                                                                  "agggaaggagggaaggaggaaggaaggaaAAT" 
##                                                                                                                                                                                                                                       >8:81903427-81903469 321_42bp 
##                                                                                                                                                                                                                        "tttgaaattggtgagatgttccttgggctgtttggtctgagg" 
##                                                                                                                                                                                                                                     >9:136857998-136858033 398_35bp 
##                                                                                                                                                                                                                               "GAGGAGCGCGGGAGGCACCAGGTGCTCAGCCTCAG" 
##                                                                                                                                                                                                                                     >9:136858034-136858050 396_16bp 
##                                                                                                                                                                                                                                                  "GCCCACGGCGGGCTTG" 
##                                                                                                                                                                                                                                         >X:3983551-3983596 614_45bp 
##                                                                                                                                                                                                                     "aggaaagagggagggagggaggaaggaaggaaggaaggaaaATTT" 
##                                                                                                                                                                                                                                       >Y:12869914-12869975 309_61bp 
##                                                                                                                                                                                                     "ttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool7
##                                                                                                                                                                                                                                       >1:18611255-18611308 156_53bp 
##                                                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                       >1:53276939-53276983 309_44bp 
##                                                                                                                                                                                                                      "CGGAACTCGCGGGGCCCGCAGGCCGGGTCTGCACAGCCGCGCTC" 
##                                                                                                                                                                                                                                        >10:6307534-6307583 201_49bp 
##                                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                     >10:10027960-10028013 2108_53bp 
##                                                                                                                                                                                                             "cagaaatagaggggcccaagcaagggattgcaactcaatttcaaaaacttctg" 
##                                                                                                                                                                                                                                     >22:46679451-46679485 1565_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 2466_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                          >5:865245-865502 777_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                         >5:4384227-4384295 139_68bp 
##                                                                                                                                                                                              "CAGAAGCTTTTAAAACCCCACATCAAACATTTAAAGGGTATTATGGTCACCTCAGGCTTTGGGTAGTC" 
##                                                                                                                                                                                                                                      >5:10649438-10649513 9655_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                       >5:66573511-66573558 116_47bp 
##                                                                                                                                                                                                                   "agggagggagggagggaggaaggaaggaaggaaAAtttaggaacaag" 
##                                                                                                                                                                                                                                     >5:131945721-131945786 682_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                     >5:131945789-131945799 669_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                     >6:104424412-104424455 132_43bp 
##                                                                                                                                                                                                                       "aggaagggagggaggaaggaaggaaggaaAATTTTTTCCCAGT" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 2547_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                    >GL000225.1:53207-53255 514_48bp 
##                                                                                                                                                                                                                  "CAGAGAGACGGGCCACCCGGAGTCCAGAATTCAGATCTGGTTTCAGAA" 
##                                                                                                                                                                                                                                       >X:13044583-13044596 388_13bp 
##                                                                                                                                                                                                                                                     "TGGCACCGCGAAG" 
##                                                                                                                                                                                                                                       >X:13044599-13044672 420_73bp 
##                                                                                                                                                                                         "CTCCGAGGGCCTGGGTCCTCTGTTCTCACGAGAGCAGCAGCCGCCCCGGCTGCCCGCGCTCCTCGCTGATTGG" 
##                                                                                                                                                                                                                                       >Y:12869918-12869975 223_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool8
##                                                                                                                                                                                                                                       >1:18611255-18611316 367_61bp 
##                                                                                                                                                                                                     "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                     >1:228610466-228610478 114_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228610482-228610537 114_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228612707-228612719 119_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228612723-228612778 120_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228614948-228614959 115_11bp 
##                                                                                                                                                                                                                                                       "CGGGGCCGCGG" 
##                                                                                                                                                                                                                                     >1:228614964-228615019 116_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228619430-228619442 122_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228619446-228619501 122_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228626107-228626118 110_11bp 
##                                                                                                                                                                                                                                                       "CGGGGCCGCGG" 
##                                                                                                                                                                                                                                     >1:228626123-228626178 111_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228628346-228628358 153_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228628362-228628417 153_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228630589-228630599 102_10bp 
##                                                                                                                                                                                                                                                        "GGGGCCGCGG" 
##                                                                                                                                                                                                                                     >1:228630604-228630657 102_53bp 
##                                                                                                                                                                                                             "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCT" 
##                                                                                                                                                                                                                                     >1:228632829-228632841 117_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228632845-228632900 117_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228635069-228635081 119_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228635085-228635140 120_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228637294-228637306 125_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228637310-228637365 128_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228639535-228639547 111_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228639551-228639606 111_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228641766-228641777 108_11bp 
##                                                                                                                                                                                                                                                       "CGGGGCCGCGG" 
##                                                                                                                                                                                                                                     >1:228641782-228641837 108_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228644008-228644018 105_10bp 
##                                                                                                                                                                                                                                                        "GGGGCCGCGG" 
##                                                                                                                                                                                                                                     >1:228644023-228644078 106_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                     >1:228646238-228646250 129_12bp 
##                                                                                                                                                                                                                                                      "CGGGGCCGCGGG" 
##                                                                                                                                                                                                                                     >1:228646254-228646309 129_55bp 
##                                                                                                                                                                                                           "GGATCGGGGACCCCCGAGCCGCTGGCCCGCGGCCTTCCCCCGGCTCCCGCGCTCC" 
##                                                                                                                                                                                                                                        >10:6307526-6307583 391_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                   >10:125774165-125774287 162_122bp 
##                                                                                                                                        "TCCGGGACCCCGCAGCGCGGCCGGTTCATGGCCGCTAGGGTGGCCGCGTCCAGCTCCCCGCTGGCCGGCAGCGCGTTCGCCCGCTGGAACCTGCGCACCGCCTCGGCCAGGGCGGCGCCCTT" 
##                                                                                                                                                                                                                                    >10:125774290-125774307 162_17bp 
##                                                                                                                                                                                                                                                 "GGTCTCCGGCGGCCCCT" 
##                                                                                                                                                                                                                                    >10:131346990-131347017 132_27bp 
##                                                                                                                                                                                                                                       "ctctccttccttcctccctccctccct" 
##                                                                                                                                                                                                                                    >10:131347243-131347276 182_33bp 
##                                                                                                                                                                                                                                 "ttccttccttccttcctccttctctcattcttt" 
##                                                                                                                                                                                                                                       >11:2457620-2457656 2155_36bp 
##                                                                                                                                                                                                                              "acaagagtggggaggggggaaggggagcaaggtttg" 
##                                                                                                                                                                                                                                      >11:65786127-65786205 136_78bp 
##                                                                                                                                                                                    "GGTGGCCGCAGCAGGGCAAAGGCGGCTGAGCCTTTCCCGGTCTGAGGTCCCCAGCCCTCCGCGCTCCACCAGCCTGGC" 
##                                                                                                                                                                                                                                    >11:113627262-113627297 164_35bp 
##                                                                                                                                                                                                                               "agggagggaggaaggaaggaagggagggagggagg" 
##                                                                                                                                                                                                                                    >11:113627447-113627478 164_31bp 
##                                                                                                                                                                                                                                   "aaggaggaaggaaggaaggaaggaaggaaaa" 
##                                                                                                                                                                                                                                      >20:29411394-29411458 392_64bp 
##                                                                                                                                                                                                  "ttctgaaaccaaatctggaccctgggctccggaatgccgatggcctgggccagcctttctctgg" 
##                                                                                                                                                                                                                                     >22:46679451-46679485 1273_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                        >4:8288864-8288951 3994_87bp 
##                                                                                                                                                                           "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                                                                                                          >5:865245-865502 541_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                     >5:10649438-10649513 17948_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                    >5:131945721-131945786 1027_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                    >5:131945789-131945799 1010_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                     >5:167774205-167774259 544_54bp 
##                                                                                                                                                                                                            "gagggagggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaAATT" 
##                                                                                                                                                                                                                                       >7:37256513-37256549 121_36bp 
##                                                                                                                                                                                                                              "gagaaggaggaaggaaggaaggaaggaaagaaggaa" 
##                                                                                                                                                                                                                                       >7:37256669-37256708 118_39bp 
##                                                                                                                                                                                                                           "agagaagggagaaggagggaaggaagaaaggaaggaaga" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 3993_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >Y:12869918-12869975 368_57bp 
##                                                                                                                                                                                                         "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $pool9
##                                                                                                                                                                                                                                       >1:18611255-18611324 366_69bp 
##                                                                                                                                                                                             "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa" 
##                                                                                                                                                                                                                                        >10:6307518-6307583 387_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                    >10:131346990-131347017 125_27bp 
##                                                                                                                                                                                                                                       "ctctccttccttcctccctccctccct" 
##                                                                                                                                                                                                                                    >10:131347241-131347276 213_35bp 
##                                                                                                                                                                                                                               "ccttccttccttccttcctccttctctcattcttt" 
##                                                                                                                                                                                                                                      >17:43665375-43665443 115_68bp 
##                                                                                                                                                                                              "ccatggggagggggcgcggtggggtgCTTTGCCCTGAGAACACAGGCCTCTGGCACCCCGGAGCCCCC" 
##                                                                                                                                                                                                                                      >22:46679451-46679485 136_34bp 
##                                                                                                                                                                                                                                "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                         >5:865245-865502 2334_257bp 
## "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                      >5:10649438-10649513 8206_75bp 
##                                                                                                                                                                                       "CGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                                                                                                     >5:131945721-131945786 780_65bp 
##                                                                                                                                                                                                 "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                                                                                                     >5:131945789-131945799 774_10bp 
##                                                                                                                                                                                                                                                        "CGCAGGTTCC" 
##                                                                                                                                                                                                                                       >7:37256513-37256549 257_36bp 
##                                                                                                                                                                                                                              "gagaaggaggaaggaaggaaggaaggaaagaaggaa" 
##                                                                                                                                                                                                                                       >7:37256753-37256803 256_50bp 
##                                                                                                                                                                                                                "agggaagggagaagggaggaggaagggaagggagaagggagggagggaaa" 
##                                                                                                                                                                                                                                     >8:22055623-22055743 3376_120bp 
##                                                                                                                                          "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                       >9:31321373-31321440 119_67bp 
##                                                                                                                                                                                               "ccagcccccaggctttaggctctcccaggcttgaaggtggggcttcaacagggacccacctccttcc" 
##                                                                                                                                                                                                                                       >Y:12869910-12869975 374_65bp 
##                                                                                                                                                                                                 "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
## 
## $PoolM
##                                                                                                                                                    >1:5991850-5991895 119_45bp 
##                                                                                                                                "CTAGGGCGCGGGGAGCCAAGGCCCAGAACATCGGTACCGCGCTCC" 
##                                                                                                                                                >1:164321420-164321491 119_71bp 
##                                                                                                      "ACGGGAATCGCGGAGCGCGGCAGCTCCCCTGCGCGCCGCCGCCGCCCTGCTCCTGGCCTCTGCAGGCGCCT" 
##                                                                                                                                                >1:168940009-168940047 384_38bp 
##                                                                                                                                       "AGGAAGGAAATTTTCCCAATTTACTAACTAAAATCTGG" 
##                                                                                                                                               >1:234742415-234742439 1097_24bp 
##                                                                                                                                                     "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                >1:240093617-240093698 148_81bp 
##                                                                                            "GGAGCGCGGGGTGGCGAGTGACAGCGGCGGTGGGGTGTCCCCAGCACTGGCCGCCAAGGCGTCTGGGGCCCCCGCGGCTGC" 
##                                                                                                                                                   >10:5813834-5813885 151_51bp 
##                                                                                                                          "ACGTGGGCGAGGAGCGCGGGCCGGGCTGCCTCTCGGGGGTGGCGGCCTTGG" 
##                                                                                                                                                   >10:5813887-5813902 150_15bp 
##                                                                                                                                                              "CCTCCCGCGGGGCTG" 
##                                                                                                                                                >10:32347230-32347346 160_116bp 
##                                                         "GGAGCGCGGGCTCGAGGCCGGCGCCGGCACGAAGCGCGCGTCCCGCCAACCCCCGGCACCCGCCGGCCTCGCTTCCCGCGCCTCGCTGCTCCGGGCCCCCGCCCTTCGCGGGTCCG" 
##                                                                                                                                                 >10:93342741-93342782 187_41bp 
##                                                                                                                                    "tggaggcagattatacagcgagatcttaaactgtctttttc" 
##                                                                                                                                              >10:108862573-108862623 1565_50bp 
##                                                                                                                           "attaatcatcgcaGACTTTGAAGGGGGAAAAAATGCCTCATGTTGAAAAC" 
##                                                                                                                                              >10:108862625-108862636 1551_11bp 
##                                                                                                                                                                  "TTGGgggtgga" 
##                                                                                                                                                 >11:93330754-93330800 123_46bp 
##                                                                                                                               "GAGCGCGGCGCAGCGCAGGTAATGGCTCCTGGCCTTCCCGGCCCCG" 
##                                                                                                                                               >11:130916242-130916335 212_93bp 
##                                                                                "CGGGCGCTGCAAGGCCCTGGGGCCCACGGACACTTACACACGCAGCGGGCAGCGGCCGGCGAAGACTGGGTCACACGCCGCCGGGAACCGCGC" 
##                                                                                                                                                 >12:47773188-47773214 382_26bp 
##                                                                                                                                                   "ggagcgcggggcgccggctgctctgg" 
##                                                                                                                                                 >12:47773215-47773231 382_16bp 
##                                                                                                                                                             "ggcTCCCGCGGCTCCG" 
##                                                                                                                                                  >12:64404619-64404626 174_7bp 
##                                                                                                                                                                      "AGAGCGA" 
##                                                                                                                                                 >12:64404627-64404666 177_39bp 
##                                                                                                                                      "TAGAGGCGCGCGGTCCCGGCCAGCACCGTCTCTGGCGTT" 
##                                                                                                                                                 >12:64404670-64404681 175_11bp 
##                                                                                                                                                                  "CTGCGGCCGTG" 
##                                                                                                                                               >12:100372360-100372458 518_98bp 
##                                                                           "tttttgaaacagggtctcactctgtcacccagcctggagtgcagtggcgagatcatagttcactgcagtgtccaactcctgggcttaagtgatcctct" 
##                                                                                                                                               >12:105330759-105330791 831_32bp 
##                                                                                                                                             "CCCCACTCGGTTCCTGGCCCCTCGCGGCCCCG" 
##                                                                                                                                               >12:118163439-118163472 262_33bp 
##                                                                                                                                            "TTTTTTTTTggggggggtgggggtagagatggg" 
##                                                                                                                                                 >15:80403871-80403944 491_73bp 
##                                                                                                    "CTGGGAGCCGAGCAGCGCGGCTCTGGCATGCTAAGTGGGCAGCACTGGGGCGCCTTTGTTCCTCGCGGCCGTC" 
##                                                                                                                                                >15:95066953-95067013 7909_60bp 
##                                                                                                                 "ccctgaaacacgtagagacacacagctagtaaactgctaaccaggattggaacttgggtc" 
##                                                                                                                                                >16:14989693-14989865 116_172bp 
## "TGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGG" 
##                                                                                                                                                 >16:35639205-35639236 122_31bp 
##                                                                                                                                              "GAGGAAGGAGTATTTGTAAAACTTGGAGAGC" 
##                                                                                                                                                 >16:50708892-50708931 198_39bp 
##                                                                                                                                      "GCGCGGCACGGAGTGCAGGCCCTGGTTTGGCCCTTGGTT" 
##                                                                                                                                                 >16:62108333-62108393 242_60bp 
##                                                                                                                 "CAGATTTTTCCCCTCTTCCCACAATACTTCCCACACTGAAATGTTTCTTTTTCCTTACTC" 
##                                                                                                                                                >16:70251562-70251701 243_139bp 
##                                  "ggagcgcggcgccggcggcccgcgAAGGGTGCGCGGCGGAAGTCGCAGAGCAggcgaccgcgcagcgcggccggggcctcgccgcctgctccggccgggccgccgccgcgctcgccgccctcggcctgtcgcgggccCG" 
##                                                                                                                                                >16:78347038-78347078 2797_40bp 
##                                                                                                                                     "TTGCGTTTTTGTGGGGGTTGGGGtaataggtttattgaga" 
##                                                                                                                                                 >17:13254784-13254854 276_70bp 
##                                                                                                       "TTTTCTTGTTGGAGTGAGGGAGGCAGCAGGGGCTTGTGTCTGTAGAGTCCTCTTGGATGACTCTCAGTGG" 
##                                                                                                                                                 >17:15786192-15786281 179_89bp 
##                                                                                    "ACCGGGAAGGCGGAgcgcggccgccagcacccccgagccgccgccggacccccgccgccccgggccgccccccgccccccgcggTCCCA" 
##                                                                                                                                                   >18:9996768-9996808 935_40bp 
##                                                                                                                                     "AGAAAAAACTCAGCATGGGTATAACCTACCCCAGTACCTC" 
##                                                                                                                                                >18:10590130-10590154 1098_24bp 
##                                                                                                                                                     "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                  >19:1600354-1600378 1123_24bp 
##                                                                                                                                                     "aggcgcccgtcactgcgcctggct" 
##                                                                                                                                                >19:48855456-48855480 1222_24bp 
##                                                                                                                                                     "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                  >2:70477225-70477246 114_21bp 
##                                                                                                                                                        "GAAGGAGGAAGGAGACAAAAT" 
##                                                                                                                                                >2:111349875-111349923 120_48bp 
##                                                                                                                             "aaaaaaaaaggaggcagagccaagtaatttcaacttcacgtctctctc" 
##                                                                                                                                               >2:119593691-119593715 1087_24bp 
##                                                                                                                                                     "agccaggcgtagtgacgggcgcct" 
##                                                                                                                                                  >3:54205770-54205813 266_43bp 
##                                                                                                                                  "AGAAAGGGAGGTAAGAAAGGGTTGCGGTGGAGGATGTCCTCTT" 
##                                                                                                                                                  >3:60181850-60181884 136_34bp 
##                                                                                                                                           "TCTGACTCCAAAAGAAATGGAGGTACACCCTCCT" 
##                                                                                                                                                >3:138508460-138508543 879_83bp 
##                                                                                          "AGGGCCTGTTGCTGATTATATTTGCTGGGCTCATCTTTCTTCTCTGTGTCCTCAGCCTTCTTATGATTAATAAGCTCCTGTAA" 
##                                                                                                                                                    >4:8288864-8288951 810_87bp 
##                                                                                      "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtct" 
##                                                                                                                                                  >4:18051824-18051868 315_44bp 
##                                                                                                                                 "tggagaaaactgacaaataTTCCTACCTCCACCATGGGAGCCAG" 
##                                                                                                                                                >4:122261613-122261700 844_87bp 
##                                                                                      "TGATTATTAGAGTAGTAGGAAGGATAATTTAGTGTTAAGAATTTGAAGGTAGAAGTTAGGTAGATGGGTTAAAAATCTGGCTTTTTC" 
##                                                                                                                                                 >5:10649439-10649513 1822_74bp 
##                                                                                                   "GGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCC" 
##                                                                                                                                                 >5:96294197-96294227 2278_30bp 
##                                                                                                                                               "ATGCATTGACTTGGGCTGTCTTTTCCTCTG" 
##                                                                                                                                                >5:115668895-115668939 139_44bp 
##                                                                                                                                 "ctaaaaagaactttatagctataagtgccttcatcaaaaagcaa" 
##                                                                                                                                                >5:131945721-131945786 511_65bp 
##                                                                                                            "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTC" 
##                                                                                                                                                >5:131945789-131945799 502_10bp 
##                                                                                                                                                                   "CGCAGGTTCC" 
##                                                                                                                                                  >6:36461862-36461889 318_27bp 
##                                                                                                                                                  "TGATTTGTAGAGAAGGAGGAAGGAAAA" 
##                                                                                                                                                  >6:39792402-39792463 228_61bp 
##                                                                                                                "GGAGCGCGGGCGGCGGCGCCGTACCTCGGGCTGCGGGAGCGCGGGCGCCCTGGGGTCCTCG" 
##                                                                                                                                                  >6:99568568-99568581 304_13bp 
##                                                                                                                                                                "GCGGCCCGCGGAG" 
##                                                                                                                                                  >6:99568582-99568627 309_45bp 
##                                                                                                                                "GACCATAGACCCAGCCCGTCCGGTAACCGCGCTCCTCGATCAAAT" 
##                                                                                                                                                >7:148667487-148667528 114_41bp 
##                                                                                                                                    "agaaagatcagctagtgtttggactgagaagtctcctctag" 
##                                                                                                                                                    >8:1974504-1974546 414_42bp 
##                                                                                                                                   "CCCTGGGGAGGGGAGCGCGGCCCTTGGTCCTCCGCCGCTGCG" 
##                                                                                                                                                    >8:4909665-4909688 148_23bp 
##                                                                                                                                                      "cacacccccggattttctccttc" 
##                                                                                                                                                 >8:22055623-22055726 220_103bp 
##                                                                      "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCT" 
##                                                                                                                                                  >8:22055727-22055743 219_16bp 
##                                                                                                                                                             "CCTTCTCTCTGGAGCC" 
##                                                                                                                                                  >8:30812217-30812293 326_76bp 
##                                                                                                 "gtgggccgcgccgggccaggggcggacgggaccggggcgggcAGGAAAGCGGCGGCCCGTCCCAGCCCCGCGCTCC" 
##                                                                                                                                                >8:66712550-66712702 3980_152bp 
##                     "GGGAAGAGAGAGGAGCGCGGGTTTCCTCGGAGGCCTGAGCGGGACGCAGCCTGCAGCCCCTCCCCGCACGGGCTGCCCCCGGCCCGCCGCTCGCGCCGCTCTGCTGGGATCCGGCGCCTTCCCCGGCTGTCCTCGGCCTCCCGCGCGCTCCG" 
##                                                                                                                                                >8:109465537-109465573 284_36bp 
##                                                                                                                                         "aaaggaaaccatttcagttttagaatgcctccattt" 
##                                                                                                                                                        >9:76145-76236 360_91bp 
##                                                                                  "GACCCAGGGATTAGGCACCAGCACCTCAGACTAGATTTTAGAGAATTACCATTCAAGAGGCAATCCTCTTCCCTTGGTTCCAATTTCAAGG" 
##                                                                                                                                                 >9:36136741-36136851 380_110bp 
##                                                               "CGCAGCCGCGGGGAGCGAGGAGCGCGCGGAGCCGGCCATGGGCAAGTCAGGTGAGCCCGCGGGCTCGCCCGCTGCGGAATGGTTCGGAACCCCGCGCTCCCGGACCTCGC" 
##                                                                                                                                                  >9:68354257-68354348 360_91bp 
##                                                                                  "CCTTGAAATTGGAACCAAGGGAAGAGGATTGCCTCTTGAATGGTAATTCTCTAAAATCTAGTCTGAGGTGCTGGTGCCTAATCCCTGGGTC" 
##                                                                                                                                                    >X:5359719-5359783 196_64bp 
##                                                                                                             "TCCGCTTTTAGAGGTAAGAGAATTATTAGAAAAAGGTTTTGCTCCCTTCATGCGGGCTATGACT" 
##                                                                                                                                                  >X:44874005-44874064 202_59bp 
##                                                                                                                  "GGAGCGCGGACACCGTCTCCCTggccggcgccgcgctcgccccgggccccgcggccggg" 
## 
## $PoolMM
##                                                              >1:234690965-234690994 120_29bp 
##                                                              "aaagagacaaccacacatgatgtgcctcc" 
##                                                             >1:234742415-234742439 3703_24bp 
##                                                                   "agccaggcgtagtgacgggcgcct" 
##                                                               >10:54011707-54011774 169_67bp 
##                        "gaaaccaaggacaagagctcagttacaaataaaggtcatgcacaaaacctcactcctctgaaaacat" 
##                                                               >10:70378639-70378682 120_43bp 
##                                                "agctgggcgtggtggcgggcgcctcgggaagctgaggcaggag" 
##                                                              >10:112050459-112050465 713_6bp 
##                                                                                     "tctgcc" 
##                                                             >10:112050466-112050494 717_28bp 
##                                                               "cccgggttttacgccattctccttcctc" 
##                                                               >11:35003588-35003634 232_46bp 
##                                             "GGAGGTAGAAGTACCTCCTTGGTTTTCCCCAGATTATTTTGCAAGT" 
##                                                               >11:65067931-65067986 185_55bp 
##                                    "GGGAGAAACACCATCCACCTCCCCCAGTTTTGTGCGTGCCTGCATGTGCCTGCAT" 
##                                                               >11:69974845-69974899 134_54bp 
##                                     "GTCCGGTTCTTATCTGAAAAAGACTAGGATGCCTCCGTCTCTaaaaaaaaaaaa" 
##                                                               >12:55273510-55273577 140_67bp 
##                        "TAAAGAAAGCAGTTAACCTACCTATTAAGGAGTTAGTCTTTTTACCTCCTTTTACATTTTTAACCTG" 
##                                                            >12:105330759-105330791 2542_32bp 
##                                                           "CCCCACTCGGTTCCTGGCCCCTCGCGGCCCCG" 
##                                                               >13:41924412-41924449 168_37bp 
##                                                      "aggagaggagatgaaggaaggaaaagcggggggaagg" 
##                                                              >14:36580240-36580293 1203_53bp 
##                                      "TTCGAAACGCCAGCAGCTCTGGGAGCCCAGCGGAGAGTCGGAGTCACTCTGGG" 
##                                                              >14:36580295-36580310 1181_15bp 
##                                                                            "CAGTGACGCCTCCCG" 
##                                                               >15:26275973-26276063 226_90bp 
## "ggaggcaacaagaaatgtacttgaagctgggaaatcagtcttgacggattcaaatttcacttctggccctttctagctgaaacaatttcc" 
##                                                              >18:10590130-10590154 3981_24bp 
##                                                                   "agccaggcgtagtgacgggcgcct" 
##                                                                >19:1600354-1600378 3820_24bp 
##                                                                   "aggcgcccgtcactgcgcctggct" 
##                                                              >19:48855456-48855480 4032_24bp 
##                                                                   "agccaggcgtagtgacgggcgcct" 
##                                                                >2:10399589-10399610 118_21bp 
##                                                                      "cgccaccaccaccaccacGAG" 
##                                                                >2:30334177-30334230 999_53bp 
##                                      "AGGCAGAGGATCTAAAAAGAACTTACCTTACCGCAGATTCTTCTGAAGGAGAG" 
##                                                                >2:70477216-70477246 868_30bp 
##                                                             "AAAAAGGAAGAAGGAGGAAGGAGACAAAAT" 
##                                                               >2:88069490-88069519 2336_29bp 
##                                                              "TCAGAGTGAAAACAACCCAGAAACACAGG" 
##                                                             >2:119593691-119593715 3805_24bp 
##                                                                   "agccaggcgtagtgacgggcgcct" 
##                                                              >2:149038924-149038977 633_53bp 
##                                      "tggggcagccaggagctcgcggggccgcggggccgcggggccgcggggccgcg" 
##                                                                >4:13436379-13436398 116_19bp 
##                                                                        "aaagggcatccaaatcagt" 
##                                                                >4:13436399-13436471 116_72bp 
##                   "aagaggaagtcaaactgtcactgttcaccaacgtcataatcctatacctagaaaaccctaaagatgcctcca" 
##                                                                >4:18671384-18671419 132_35bp 
##                                                        "atattttttgggggggatgggggtgttgttttttt" 
##                                                                >4:78125849-78125923 122_74bp 
##                 "ggaggcaatctgcccgttattggagcttgaatgccatgctgggagaaccactgccgtcttcagagctgtcaggc" 
##                                                                >5:84522157-84522201 582_44bp 
##                                               "ATCTTAAAAATTAGTAAAACTGATAGCTAAAATCTGGGGATGGG" 
##                                                              >5:125362225-125362268 134_43bp 
##                                                "aaagaacatctttatttctgcctccatttcgttatgtagccag" 
##                                                             >5:143586716-143586775 2773_59bp 
##                                "GTCTTAGAAACAAAATATGTTCCTCTTTGGTTCCAGATGCTTGGGTTTCTAGAGTCTGG" 
##                                                                >6:54751950-54752026 468_76bp 
##               "ACCCAAATCTGAAGTTCCCATCAAATAATTTTGAATACCAATCAACTGCTGATTTATATTTGATTTCAGGAACTTC" 
##                                                              >6:125050045-125050092 272_47bp 
##                                            "GGAGGTAGAGGAGGTGATAGCAGTTCTTTATGGAAGAGAGGAGAGAT" 
##                                                              >6:162134756-162134804 329_48bp 
##                                           "ATGGAGGCAGAGAGTGCCAAAAAGAAAGAGTGGATGTCAGCTCATTCT" 
##                                                                >7:45596896-45596960 127_64bp 
##                           "TGGAGGCAGGGGAGCAGACACACTGGGGAGTTTGGCGGTGGTTTTCTTTTTGTTTCTTCCTGGG" 
##                                                              >7:147628581-147628618 122_37bp 
##                                                      "aaggcaacaactagcatgatgaagaaaacagtacctc" 
##                                                                 >8:1974504-1974546 1773_42bp 
##                                                 "CCCTGGGGAGGGGAGCGCGGCCCTTGGTCCTCCGCCGCTGCG" 
##                                                                >X:78458592-78458645 382_53bp 
##                                      "acaaatagaatttaaagaaaaccaaacatcatcttatacttgataatgcctcc" 
## 
## $Undetermined
##                                                                                                                                                                                                                                                                                                                                                                                      >1:18611255-18611326 275_71bp 
##                                                                                                                                                                                                                                                                                                                                          "agaaagggagagaaggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagg" 
##                                                                                                                                                                                                                                                                                                                                                                                       >10:6307518-6307583 307_65bp 
##                                                                                                                                                                                                                                                                                                                                                "ttccttccttccttccttccttccttccttccttccttccttccttccttcctccttctctccct" 
##                                                                                                                                                                                                                                                                                                                                                                                     >10:10027960-10028013 152_53bp 
##                                                                                                                                                                                                                                                                                                                                                            "cagaaatagaggggcccaagcaagggattgcaactcaatttcaaaaacttctg" 
##                                                                                                                                                                                                                                                                                                                                                                                   >10:100122122-100122149 142_27bp 
##                                                                                                                                                                                                                                                                                                                                                                                      "agggagggaggaaggaaggaaggaagg" 
##                                                                                                                                                                                                                                                                                                                                                                                   >10:100122170-100122185 120_15bp 
##                                                                                                                                                                                                                                                                                                                                                                                                  "aggaaggaaggaagg" 
##                                                                                                                                                                                                                                                                                                                                                                                     >15:95066953-95067013 227_60bp 
##                                                                                                                                                                                                                                                                                                                                                     "ccctgaaacacgtagagacacacagctagtaaactgctaaccaggattggaacttgggtc" 
##                                                                                                                                                                                                                                                                                                                                                                                    >16:14989690-14989868 156_178bp 
##                                                                                                                                                                                                                               "AGCTGCAGGCAACGCACGCGGCGCAGCAGCCCCTCCCGCAGCAGCAGCACCGCCTCTCCAGCTTCAGCCAGCGCGCTCAGCGGGCGCAGCTGCACGAAGGGCACAAAGTCCGGCGCCACGGCGGGCTCCCGCTCCCCGGGAGTCACCCACAGCCGATTGGCAGCCACGTCCAGGGCCA" 
##                                                                                                                                                                                                                                                                                                                                                                                   >19:35358874-35359135 3973_261bp 
##                                                                                                                                            "ACCAGTGGCCACCACCATGGATACAGGCCCCGACCAGTCCTACTTCTCCGGCAATCACTGGTTCGTCTTCTCGGTGTACCTTCTCACTTTCCTGGTGGGGCTCCCCCTCAACCTGCTGGCCCTGGTGGTCTTCGTGGGCAAGCTGCAGCGCCGCCCGGTGGCCGTGGACGTGCTCCTGCTCAACCTGACCGCCTCGGACCTGCTCCTGCTGCTGTTCCTGCCTTTCCGCATGGTGGAGGCAGCCAATGGCATGCACTGGCC" 
##                                                                                                                                                                                                                                                                                                                                                                                   >19:35371343-35371604 3969_261bp 
##                                                                                                                                            "ACCAGTGGCCACCACCATGGATACAGGCCCCGACCAGTCCTACTTCTCCGGCAATCACTGGTTCGTCTTCTCGGTGTACCTTCTCACTTTCCTGGTGGGGCTCCCCCTCAACCTGCTGGCCCTGGTGGTCTTCGTGGGCAAGCTGCGGTGCCGCCCGGTGGCCGTGGACGTGCTCCTGCTCAACCTGACCGCCTCGGACCTGCTCCTGCTGCTGTTCCTGCCTTTCCGCATGGTGGAGGCAGCCAATGGCATGCACTGGCC" 
##                                                                                                                                                                                                                                                                                                                                                                                    >2:32916232-32916632 1964_400bp 
## "ggggggggtggggggggggcgggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggagggaggggggggtgagagggggggggggggggggggggggggggggggggggggggggggggggggagggggggggggggggggggggggggggggggggggggggagggggggggggggggggggggggggggggggaggggggggggggaggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggagggggggggggggggggggggggcgggggcggggggggggagggggggggggggggggggggggggggnnnnnnn" 
##                                                                                                                                                                                                                                                                                                                                                                                     >22:46679451-46679485 299_34bp 
##                                                                                                                                                                                                                                                                                                                                                                               "GGAGCGCGGATCGGCACGGGCTCTGGGCTCCCCG" 
##                                                                                                                                                                                                                                                                                                                                                                                      >3:60181850-60181902 178_52bp 
##                                                                                                                                                                                                                                                                                                                                                             "TCTGACTCCAAAAGAAATGGAGGTACACCCTCCTATATATATCTCTACCTGT" 
##                                                                                                                                                                                                                                                                                                                                                                                       >4:8288864-8288955 2094_91bp 
##                                                                                                                                                                                                                                                                                                                      "ccCACCCCCAAATTttccttccttccttccgtccgtccttccttccttccttccttccttccttccttcctcccttcctcccCCtctctct" 
##                                                                                                                                                                                                                                                                                                                                                                                        >5:865245-865502 2611_257bp 
##                                                                                                                                                "CGAGGCCGCGACCCAAGGACATCTGTGGAAACCGACCTCCACAACAGCACCGCTGCCCATGCAGCCTCCAGCCTTCCCACAACTACAATGCTGCCCACTACCTCGTCTAGACGTCACACTGACTGTGCTGGGGTCTCTGGGGATGCGGCGTGGGTGGGGGCATCTCACCCAGGTGGTGCTGGTCCCTCTCGGAGGCGTTGGACAGGGAGCTGAGGTTGGACGACGGCCGAGAGCCGCCGCGCTCCGCCTGTGCTTCG" 
##                                                                                                                                                                                                                                                                                                                                                                                    >5:10649430-10649514 16571_84bp 
##                                                                                                                                                                                                                                                                                                                             "AAGCGGCGCGGAAGCCCGCGGGCTCCAAGAACTGCCTGCAGAGGCTCACAGACTGCGTGCTGTCCGTGCTGACGCCGCGCTCCG" 
##                                                                                                                                                                                                                                                                                                                                                                                    >5:119023122-119023140 150_18bp 
##                                                                                                                                                                                                                                                                                                                                                                                               "ttaactttgaaaacaatc" 
##                                                                                                                                                                                                                                                                                                                                                                                    >5:119023143-119023175 150_32bp 
##                                                                                                                                                                                                                                                                                                                                                                                 "tgaggtacagttggccctccttatctataagt" 
##                                                                                                                                                                                                                                                                                                                                                                                   >5:131945721-131945788 1194_67bp 
##                                                                                                                                                                                                                                                                                                                                              "GGGAAAACGGAGGAGCGCGGCAGCCGCCCAGCCTTCCTATAGGGGCCCAGTGGTTTCTGGCCTTCTG" 
##                                                                                                                                                                                                                                                                                                                                                                                   >5:131945789-131945799 1078_10bp 
##                                                                                                                                                                                                                                                                                                                                                                                                       "CGCAGGTTCC" 
##                                                                                                                                                                                                                                                                                                                                                                                    >5:143586716-143586735 105_19bp 
##                                                                                                                                                                                                                                                                                                                                                                                              "GTCTTAGAAACAAAATATG" 
##                                                                                                                                                                                                                                                                                                                                                                                    >5:143586736-143586766 105_30bp 
##                                                                                                                                                                                                                                                                                                                                                                                   "TCCTCTTTGGTTCCAGATGCTTGGGTTTCT" 
##                                                                                                                                                                                                                                                                                                                                                                                      >6:54725892-54725921 239_29bp 
##                                                                                                                                                                                                                                                                                                                                                                                    "gttttctgagtatctataacaactatttc" 
##                                                                                                                                                                                                                                                                                                                                                                                      >6:54725998-54726020 239_22bp 
##                                                                                                                                                                                                                                                                                                                                                                                           "tgggtatctataacaactattt" 
##                                                                                                                                                                                                                                                                                                                                                                                    >8:22055623-22055743 3883_120bp 
##                                                                                                                                                                                                                                                                                         "CCCACCCCCAGGTTTTCTCTACCTTCACAGCCACCCCCGCCTGGCTGCAGCAGCTCAGCCTGTGTTCTGTCTCCCTTCTCAGCCACCTGCCTCCTTCCTTCCTCCCTTCTCTCTGGAGCC" 
##                                                                                                                                                                                                                                                                                                                                                                                     >8:66712550-66712695 188_145bp 
##                                                                                                                                                                                                                                                                "GGGAAGAGAGAGGAGCGCGGGTTTCCTCGGAGGCCTGAGCGGGACGCAGCCTGCAGCCCCTCCCCGCACGGGCTGCCCCCGGCCCGCCGCTCGCGCCGCTCTGCTGGGATCCGGCGCCTTCCCCGGCTGTCCTCGGCCTCCCGCG" 
##                                                                                                                                                                                                                                                                                                                                                                                       >8:66712696-66712702 181_6bp 
##                                                                                                                                                                                                                                                                                                                                                                                                           "GCTCCG" 
##                                                                                                                                                                                                                                                                                                                                                                                      >X:82446629-82446671 185_42bp 
##                                                                                                                                                                                                                                                                                                                                                                       "atgaggaaaaaacagagcaaaagcgcagaaaatttcaaaaac" 
##                                                                                                                                                                                                                                                                                                                                                                                      >X:82446673-82446687 183_14bp 
##                                                                                                                                                                                                                                                                                                                                                                                                   "gaatacctcttctc" 
##                                                                                                                                                                                                                                                                                                                                                                                      >Y:12869918-12869975 178_57bp 
##                                                                                                                                                                                                                                                                                                                                                        "ttccttccttccttccttccttccttccttccttccttccttcctccttctctccct"

Look at the origin of the off-target reads

If we look at the similarity of the genomic locations with the amplicons we should be able to track down which primer was responsible for which off-target region. The primers are 16-26 bp in length so I will use the 20bp at the termini to do this classification.

In these heatmaps, the seq names along the bottom are the target amplicons and the ones along the right are the off-target regions.

The deeper the red, the smaller the sequence edit distance.

# amplicon termini

x <- readLines("amplicons_hg38.bed.starts.fa")
n=length(x)
amp_st <- x[(1:(n/2))*2]
names(amp_st) <- x[((1:(n/2))*2)-1]

x <- readLines("amplicons_hg38.bed.ends.fa")
n=length(x)
amp_en <- x[(1:(n/2))*2]
names(amp_en) <- x[((1:(n/2))*2)-1]

amp <-c(amp_st,amp_en)

# seq termini
mystarts <- list.files("fastq/",pattern=".bedgraph.offtarget.starts.fa$",full.names=TRUE)
myends <- list.files("fastq/",pattern=".bedgraph.offtarget.ends.fa$",full.names=TRUE)

idxs <- grep("ool",mystarts)

lapply(idxs, function(z) {
  mystart <- mystarts[z]
  x <- readLines(mystart)
  n=length(x)
  st <- x[(1:(n/2))*2]
  names(st) <- x[((1:(n/2))*2)-1]
  myend <- myends[z]
  x <- readLines(myend)
  n=length(x)
  en <- x[(1:(n/2))*2]
  names(en) <- x[((1:(n/2))*2)-1]
  seq <-c(st,en)
  adist(seq,amp)
  colfunc <- colorRampPalette(c("red", "white"))
  heatmap.2(adist(seq,amp),col=colfunc(50),trace="none",scale="none",margin=c(15,20),main=names(oft2)[z])
})

## [[1]]
## [[1]]$rowInd
##  [1] 13  4  8  1 17  7 15 14  2 16 11 18  9 12  3  6  5 10
## 
## [[1]]$colInd
##  [1]  8  3 11 12 14  7  9  5  2  6  4 10 13  1
## 
## [[1]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[1]]$carpet
##                      >18611255-18611316 259_61BP >4:8288864-8288951 2355_87BP
## >128241036-128241347                          17                           15
## >2:25168373-25168611                          17                           15
## >25161598-25161833                            14                           13
## >25168373-25168611                            16                           14
## >78358469-78358619                             8                            7
## >7:128241036-1282413                           7                            5
## >24283548-24283843                            14                           12
## >7:24283548-24283843                          14                           11
## >2:25161598-25161833                          10                           12
## >7:24283796-24283936                          12                           13
## >6:31575210-31575467                          13                           11
## >24283796-24283936                            12                            8
## >31575210-31575467                            10                           11
## >17:78358469-7835861                          10                           12
##                      >8:22055623-22055743 4150_120BP
## >128241036-128241347                              14
## >2:25168373-25168611                              15
## >25161598-25161833                                12
## >25168373-25168611                                15
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >2:25161598-25161833                              11
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >24283796-24283936                                10
## >31575210-31575467                                11
## >17:78358469-7835861                              12
##                      >1:18611255-18611316 259_61BP >8288864-8288951 2355_87BP
## >128241036-128241347                             4                          6
## >2:25168373-25168611                            10                         11
## >25161598-25161833                              11                         12
## >25168373-25168611                               8                         11
## >78358469-78358619                              16                         15
## >7:128241036-1282413                            15                         16
## >24283548-24283843                              11                         11
## >7:24283548-24283843                             9                          9
## >2:25161598-25161833                            15                         13
## >7:24283796-24283936                            12                         11
## >6:31575210-31575467                            12                         12
## >24283796-24283936                              13                         14
## >31575210-31575467                              12                         14
## >17:78358469-7835861                            14                         13
##                      >5:131945721-131945786 896_65BP >4550782-4550844 593_62BP
## >128241036-128241347                              11                        12
## >2:25168373-25168611                               8                        11
## >25161598-25161833                                10                         9
## >25168373-25168611                                10                        11
## >78358469-78358619                                16                        15
## >7:128241036-1282413                              16                        17
## >24283548-24283843                                10                        12
## >7:24283548-24283843                              12                        10
## >2:25161598-25161833                              13                        15
## >7:24283796-24283936                              13                        14
## >6:31575210-31575467                              14                        17
## >24283796-24283936                                13                        14
## >31575210-31575467                                16                        14
## >17:78358469-7835861                              14                        17
##                      >22055623-22055743 4150_120BP
## >128241036-128241347                             6
## >2:25168373-25168611                            10
## >25161598-25161833                               9
## >25168373-25168611                               9
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >2:25161598-25161833                            11
## >7:24283796-24283936                            10
## >6:31575210-31575467                             8
## >24283796-24283936                              12
## >31575210-31575467                              11
## >17:78358469-7835861                            13
##                      >11:65786127-65786205 111_78BP >65786127-65786205 111_78BP
## >128241036-128241347                             11                          10
## >2:25168373-25168611                              9                          11
## >25161598-25161833                                9                           8
## >25168373-25168611                               13                          10
## >78358469-78358619                               12                          13
## >7:128241036-1282413                             15                          13
## >24283548-24283843                               10                          11
## >7:24283548-24283843                             11                          12
## >2:25161598-25161833                             11                           8
## >7:24283796-24283936                              9                           8
## >6:31575210-31575467                             12                          13
## >24283796-24283936                               11                          14
## >31575210-31575467                               14                          12
## >17:78358469-7835861                             12                          13
##                      >13044599-13044672 174_73BP >865245-865502 767_257BP
## >128241036-128241347                           9                        9
## >2:25168373-25168611                          11                       12
## >25161598-25161833                             9                       11
## >25168373-25168611                             9                       10
## >78358469-78358619                            12                       15
## >7:128241036-1282413                          14                       15
## >24283548-24283843                            10                       10
## >7:24283548-24283843                          13                       12
## >2:25161598-25161833                          12                       10
## >7:24283796-24283936                          12                       12
## >6:31575210-31575467                          12                       13
## >24283796-24283936                            13                       13
## >31575210-31575467                            12                       14
## >17:78358469-7835861                          15                       14
##                      >X:13044599-13044672 174_73BP
## >128241036-128241347                            15
## >2:25168373-25168611                            14
## >25161598-25161833                              12
## >25168373-25168611                              12
## >78358469-78358619                              10
## >7:128241036-1282413                            11
## >24283548-24283843                              11
## >7:24283548-24283843                            10
## >2:25161598-25161833                            13
## >7:24283796-24283936                            11
## >6:31575210-31575467                            16
## >24283796-24283936                              13
## >31575210-31575467                              12
## >17:78358469-7835861                            14
##                      >131945721-131945786 896_65BP >17:4550782-4550844 593_62BP
## >128241036-128241347                            11                           11
## >2:25168373-25168611                            12                           10
## >25161598-25161833                              12                           13
## >25168373-25168611                              13                           12
## >78358469-78358619                              11                           10
## >7:128241036-1282413                            11                           10
## >24283548-24283843                              10                           11
## >7:24283548-24283843                             7                           11
## >2:25161598-25161833                            10                           15
## >7:24283796-24283936                            14                           14
## >6:31575210-31575467                            10                           10
## >24283796-24283936                              10                           10
## >31575210-31575467                               9                           13
## >17:78358469-7835861                            11                           13
##                      >5:10649438-10649513 15302_75BP >5:865245-865502 767_257BP
## >128241036-128241347                              14                         11
## >2:25168373-25168611                               9                         10
## >25161598-25161833                                15                         11
## >25168373-25168611                                16                         13
## >78358469-78358619                                13                         14
## >7:128241036-1282413                              13                         14
## >24283548-24283843                                10                         12
## >7:24283548-24283843                              11                         13
## >2:25161598-25161833                              12                         11
## >7:24283796-24283936                              11                         14
## >6:31575210-31575467                              13                         13
## >24283796-24283936                                13                         12
## >31575210-31575467                                14                         12
## >17:78358469-7835861                              13                         10
##                      >10649438-10649513 15302_75BP
## >128241036-128241347                            12
## >2:25168373-25168611                             8
## >25161598-25161833                              10
## >25168373-25168611                              14
## >78358469-78358619                              16
## >7:128241036-1282413                            15
## >24283548-24283843                              10
## >7:24283548-24283843                            12
## >2:25161598-25161833                            11
## >7:24283796-24283936                            14
## >6:31575210-31575467                            15
## >24283796-24283936                              14
## >31575210-31575467                              13
## >17:78358469-7835861                            12
## 
## [[1]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 22.36068 
## 
## [[1]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 26.28688 
## 
## [[1]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[1]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[1]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[1]]$layout
## [[1]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[1]]$layout$lhei
## [1] 1.5 4.0
## 
## [[1]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[2]]
## [[2]]$rowInd
##  [1]  9 12 10  2  7 11  1  3  6 13 14  5  4  8
## 
## [[2]]$colInd
##  [1]  3  8 11 12  7 14  4  6  5  9  2  1 10 13
## 
## [[2]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[2]]$carpet
##                      >131945721-131945786 1352_65BP
## >2:25168373-25168611                             12
## >128241036-128241347                             11
## >25161598-25161833                               12
## >25168373-25168611                               13
## >7:128241036-1282413                             11
## >78358469-78358619                               11
## >6:31575210-31575467                             10
## >7:24283796-24283936                             14
## >7:24283548-24283843                              7
## >24283548-24283843                               10
## >2:25161598-25161833                             10
## >17:78358469-7835861                             11
## >24283796-24283936                               10
## >31575210-31575467                                9
##                      >78422580-78422696 168_116BP >14989690-14989869 168_179BP
## >2:25168373-25168611                           13                           12
## >128241036-128241347                           13                           12
## >25161598-25161833                             14                           11
## >25168373-25168611                             11                           13
## >7:128241036-1282413                            9                           10
## >78358469-78358619                             10                            8
## >6:31575210-31575467                           12                           10
## >7:24283796-24283936                           14                           11
## >7:24283548-24283843                           10                           12
## >24283548-24283843                             11                           10
## >2:25161598-25161833                           12                           11
## >17:78358469-7835861                            8                           12
## >24283796-24283936                              6                           12
## >31575210-31575467                              9                           13
##                      >4:8288864-8288951 3647_87BP
## >2:25168373-25168611                           15
## >128241036-128241347                           15
## >25161598-25161833                             13
## >25168373-25168611                             14
## >7:128241036-1282413                            5
## >78358469-78358619                              7
## >6:31575210-31575467                           11
## >7:24283796-24283936                           13
## >7:24283548-24283843                           11
## >24283548-24283843                             12
## >2:25161598-25161833                           12
## >17:78358469-7835861                           12
## >24283796-24283936                              8
## >31575210-31575467                             11
##                      >8:22055623-22055743 3445_120BP
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25161598-25161833                                12
## >25168373-25168611                                15
## >7:128241036-1282413                               7
## >78358469-78358619                                 7
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >7:24283548-24283843                              11
## >24283548-24283843                                12
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
## >24283796-24283936                                10
## >31575210-31575467                                11
##                      >22055623-22055743 3445_120BP
## >2:25168373-25168611                            10
## >128241036-128241347                             6
## >25161598-25161833                               9
## >25168373-25168611                               9
## >7:128241036-1282413                            13
## >78358469-78358619                              10
## >6:31575210-31575467                             8
## >7:24283796-24283936                            10
## >7:24283548-24283843                            13
## >24283548-24283843                              11
## >2:25161598-25161833                            11
## >17:78358469-7835861                            13
## >24283796-24283936                              12
## >31575210-31575467                              11
##                      >16:14989690-14989869 168_179BP
## >2:25168373-25168611                              12
## >128241036-128241347                               9
## >25161598-25161833                                 9
## >25168373-25168611                                10
## >7:128241036-1282413                              11
## >78358469-78358619                                13
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >7:24283548-24283843                              10
## >24283548-24283843                                12
## >2:25161598-25161833                               9
## >17:78358469-7835861                              14
## >24283796-24283936                                12
## >31575210-31575467                                10
##                      >4:78422580-78422696 168_116BP
## >2:25168373-25168611                             14
## >128241036-128241347                             13
## >25161598-25161833                               12
## >25168373-25168611                               14
## >7:128241036-1282413                             10
## >78358469-78358619                               14
## >6:31575210-31575467                             16
## >7:24283796-24283936                             13
## >7:24283548-24283843                              9
## >24283548-24283843                               11
## >2:25161598-25161833                             10
## >17:78358469-7835861                             11
## >24283796-24283936                               11
## >31575210-31575467                               10
##                      >5:131945721-131945786 1352_65BP
## >2:25168373-25168611                                8
## >128241036-128241347                               11
## >25161598-25161833                                 10
## >25168373-25168611                                 10
## >7:128241036-1282413                               16
## >78358469-78358619                                 16
## >6:31575210-31575467                               14
## >7:24283796-24283936                               13
## >7:24283548-24283843                               12
## >24283548-24283843                                 10
## >2:25161598-25161833                               13
## >17:78358469-7835861                               14
## >24283796-24283936                                 13
## >31575210-31575467                                 16
##                      >8288864-8288951 3647_87BP >865245-865502 1648_257BP
## >2:25168373-25168611                         11                        12
## >128241036-128241347                          6                         9
## >25161598-25161833                           12                        11
## >25168373-25168611                           11                        10
## >7:128241036-1282413                         16                        15
## >78358469-78358619                           15                        15
## >6:31575210-31575467                         12                        13
## >7:24283796-24283936                         11                        12
## >7:24283548-24283843                          9                        12
## >24283548-24283843                           11                        10
## >2:25161598-25161833                         13                        10
## >17:78358469-7835861                         13                        14
## >24283796-24283936                           14                        13
## >31575210-31575467                           14                        14
##                      >5:10649438-10649513 6749_75BP >5:865245-865502 1648_257BP
## >2:25168373-25168611                              9                          10
## >128241036-128241347                             14                          11
## >25161598-25161833                               15                          11
## >25168373-25168611                               16                          13
## >7:128241036-1282413                             13                          14
## >78358469-78358619                               13                          14
## >6:31575210-31575467                             13                          13
## >7:24283796-24283936                             11                          14
## >7:24283548-24283843                             11                          13
## >24283548-24283843                               10                          12
## >2:25161598-25161833                             12                          11
## >17:78358469-7835861                             13                          10
## >24283796-24283936                               13                          12
## >31575210-31575467                               14                          12
##                      >10649438-10649513 6749_75BP
## >2:25168373-25168611                            8
## >128241036-128241347                           12
## >25161598-25161833                             10
## >25168373-25168611                             14
## >7:128241036-1282413                           15
## >78358469-78358619                             16
## >6:31575210-31575467                           15
## >7:24283796-24283936                           14
## >7:24283548-24283843                           12
## >24283548-24283843                             10
## >2:25161598-25161833                           11
## >17:78358469-7835861                           12
## >24283796-24283936                             14
## >31575210-31575467                             13
## 
## [[2]]$rowDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 19 
## 
## [[2]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 20.27313 
## 
## [[2]]$breaks
##  [1]  5.00  5.22  5.44  5.66  5.88  6.10  6.32  6.54  6.76  6.98  7.20  7.42
## [13]  7.64  7.86  8.08  8.30  8.52  8.74  8.96  9.18  9.40  9.62  9.84 10.06
## [25] 10.28 10.50 10.72 10.94 11.16 11.38 11.60 11.82 12.04 12.26 12.48 12.70
## [37] 12.92 13.14 13.36 13.58 13.80 14.02 14.24 14.46 14.68 14.90 15.12 15.34
## [49] 15.56 15.78 16.00
## 
## [[2]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[2]]$colorTable
##      low  high   color
## 1   5.00  5.22 #FF0000
## 2   5.22  5.44 #FF0505
## 3   5.44  5.66 #FF0A0A
## 4   5.66  5.88 #FF0F0F
## 5   5.88  6.10 #FF1414
## 6   6.10  6.32 #FF1A1A
## 7   6.32  6.54 #FF1F1F
## 8   6.54  6.76 #FF2424
## 9   6.76  6.98 #FF2929
## 10  6.98  7.20 #FF2E2E
## 11  7.20  7.42 #FF3434
## 12  7.42  7.64 #FF3939
## 13  7.64  7.86 #FF3E3E
## 14  7.86  8.08 #FF4343
## 15  8.08  8.30 #FF4848
## 16  8.30  8.52 #FF4E4E
## 17  8.52  8.74 #FF5353
## 18  8.74  8.96 #FF5858
## 19  8.96  9.18 #FF5D5D
## 20  9.18  9.40 #FF6262
## 21  9.40  9.62 #FF6868
## 22  9.62  9.84 #FF6D6D
## 23  9.84 10.06 #FF7272
## 24 10.06 10.28 #FF7777
## 25 10.28 10.50 #FF7C7C
## 26 10.50 10.72 #FF8282
## 27 10.72 10.94 #FF8787
## 28 10.94 11.16 #FF8C8C
## 29 11.16 11.38 #FF9191
## 30 11.38 11.60 #FF9696
## 31 11.60 11.82 #FF9C9C
## 32 11.82 12.04 #FFA1A1
## 33 12.04 12.26 #FFA6A6
## 34 12.26 12.48 #FFABAB
## 35 12.48 12.70 #FFB0B0
## 36 12.70 12.92 #FFB6B6
## 37 12.92 13.14 #FFBBBB
## 38 13.14 13.36 #FFC0C0
## 39 13.36 13.58 #FFC5C5
## 40 13.58 13.80 #FFCACA
## 41 13.80 14.02 #FFD0D0
## 42 14.02 14.24 #FFD5D5
## 43 14.24 14.46 #FFDADA
## 44 14.46 14.68 #FFDFDF
## 45 14.68 14.90 #FFE4E4
## 46 14.90 15.12 #FFEAEA
## 47 15.12 15.34 #FFEFEF
## 48 15.34 15.56 #FFF4F4
## 49 15.56 15.78 #FFF9F9
## 50 15.78 16.00 #FFFFFF
## 
## [[2]]$layout
## [[2]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[2]]$layout$lhei
## [1] 1.5 4.0
## 
## [[2]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[3]]
## [[3]]$rowInd
## [1] 1 4 6 7 3 2 5 8
## 
## [[3]]$colInd
##  [1]  7 14  3  8 12 10 13  6  4  5  9 11  2  1
## 
## [[3]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[3]]$carpet
##                      >4:8288864-8288951 403_87BP >8:22055623-22055726 402_103BP
## >7:128241036-1282413                           5                              7
## >78358469-78358619                             7                              7
## >2:25168373-25168611                          15                             15
## >128241036-128241347                          15                             14
## >25168373-25168611                            14                             15
## >24283796-24283936                             8                             10
## >31575210-31575467                            11                             11
## >7:24283796-24283936                          13                             12
## >6:31575210-31575467                          11                             13
## >7:24283548-24283843                          11                             11
## >24283548-24283843                            12                             12
## >25161598-25161833                            13                             12
## >2:25161598-25161833                          12                             11
## >17:78358469-7835861                          12                             12
##                      >22055623-22055726 402_103BP >8288864-8288951 403_87BP
## >7:128241036-1282413                           14                        16
## >78358469-78358619                             14                        15
## >2:25168373-25168611                            9                        11
## >128241036-128241347                            9                         6
## >25168373-25168611                              9                        11
## >24283796-24283936                             12                        14
## >31575210-31575467                             12                        14
## >7:24283796-24283936                           12                        11
## >6:31575210-31575467                           13                        12
## >7:24283548-24283843                            9                         9
## >24283548-24283843                              9                        11
## >25161598-25161833                             12                        12
## >2:25161598-25161833                           14                        13
## >17:78358469-7835861                           14                        13
##                      >5:10649439-10649513 955_74BP >5:865245-865490 213_245BP
## >7:128241036-1282413                            13                         14
## >78358469-78358619                              12                         14
## >2:25168373-25168611                             7                         10
## >128241036-128241347                            13                         11
## >25168373-25168611                              16                         13
## >24283796-24283936                              11                         12
## >31575210-31575467                              12                         12
## >7:24283796-24283936                            11                         14
## >6:31575210-31575467                            14                         13
## >7:24283548-24283843                            10                         13
## >24283548-24283843                              10                         12
## >25161598-25161833                              14                         11
## >2:25161598-25161833                            11                         11
## >17:78358469-7835861                            12                         10
##                      >10649439-10649513 955_74BP >865245-865490 213_245BP
## >7:128241036-1282413                          15                       16
## >78358469-78358619                            16                       15
## >2:25168373-25168611                           8                        9
## >128241036-128241347                          12                       14
## >25168373-25168611                            14                       16
## >24283796-24283936                            14                       13
## >31575210-31575467                            13                       13
## >7:24283796-24283936                          14                       15
## >6:31575210-31575467                          15                       15
## >7:24283548-24283843                          12                       11
## >24283548-24283843                            10                       12
## >25161598-25161833                            10                       11
## >2:25161598-25161833                          11                       11
## >17:78358469-7835861                          12                       12
## 
## [[3]]$rowDendrogram
## 'dendrogram' with 2 branches and 8 members total, at height 18.68154 
## 
## [[3]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 19.07878 
## 
## [[3]]$breaks
##  [1]  5.00  5.22  5.44  5.66  5.88  6.10  6.32  6.54  6.76  6.98  7.20  7.42
## [13]  7.64  7.86  8.08  8.30  8.52  8.74  8.96  9.18  9.40  9.62  9.84 10.06
## [25] 10.28 10.50 10.72 10.94 11.16 11.38 11.60 11.82 12.04 12.26 12.48 12.70
## [37] 12.92 13.14 13.36 13.58 13.80 14.02 14.24 14.46 14.68 14.90 15.12 15.34
## [49] 15.56 15.78 16.00
## 
## [[3]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[3]]$colorTable
##      low  high   color
## 1   5.00  5.22 #FF0000
## 2   5.22  5.44 #FF0505
## 3   5.44  5.66 #FF0A0A
## 4   5.66  5.88 #FF0F0F
## 5   5.88  6.10 #FF1414
## 6   6.10  6.32 #FF1A1A
## 7   6.32  6.54 #FF1F1F
## 8   6.54  6.76 #FF2424
## 9   6.76  6.98 #FF2929
## 10  6.98  7.20 #FF2E2E
## 11  7.20  7.42 #FF3434
## 12  7.42  7.64 #FF3939
## 13  7.64  7.86 #FF3E3E
## 14  7.86  8.08 #FF4343
## 15  8.08  8.30 #FF4848
## 16  8.30  8.52 #FF4E4E
## 17  8.52  8.74 #FF5353
## 18  8.74  8.96 #FF5858
## 19  8.96  9.18 #FF5D5D
## 20  9.18  9.40 #FF6262
## 21  9.40  9.62 #FF6868
## 22  9.62  9.84 #FF6D6D
## 23  9.84 10.06 #FF7272
## 24 10.06 10.28 #FF7777
## 25 10.28 10.50 #FF7C7C
## 26 10.50 10.72 #FF8282
## 27 10.72 10.94 #FF8787
## 28 10.94 11.16 #FF8C8C
## 29 11.16 11.38 #FF9191
## 30 11.38 11.60 #FF9696
## 31 11.60 11.82 #FF9C9C
## 32 11.82 12.04 #FFA1A1
## 33 12.04 12.26 #FFA6A6
## 34 12.26 12.48 #FFABAB
## 35 12.48 12.70 #FFB0B0
## 36 12.70 12.92 #FFB6B6
## 37 12.92 13.14 #FFBBBB
## 38 13.14 13.36 #FFC0C0
## 39 13.36 13.58 #FFC5C5
## 40 13.58 13.80 #FFCACA
## 41 13.80 14.02 #FFD0D0
## 42 14.02 14.24 #FFD5D5
## 43 14.24 14.46 #FFDADA
## 44 14.46 14.68 #FFDFDF
## 45 14.68 14.90 #FFE4E4
## 46 14.90 15.12 #FFEAEA
## 47 15.12 15.34 #FFEFEF
## 48 15.34 15.56 #FFF4F4
## 49 15.56 15.78 #FFF9F9
## 50 15.78 16.00 #FFFFFF
## 
## [[3]]$layout
## [[3]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[3]]$layout$lhei
## [1] 1.5 4.0
## 
## [[3]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[4]]
## [[4]]$rowInd
##  [1] 25  8 13 21  3 15  9 12 10 14 24 23 11 16 30 19  6  7 18  4 20 22  2 27  5
## [26] 29  1 28 17 26
## 
## [[4]]$colInd
##  [1]  8 11 12  3  9  5 14  7  4 13 10  2  6  1
## 
## [[4]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[4]]$carpet
##                      >58306257-58306325 156_68BP >4:8288864-8288951 608_87BP
## >128241036-128241347                          15                          15
## >25161598-25161833                            14                          13
## >25168373-25168611                            14                          14
## >2:25168373-25168611                          15                          15
## >24283548-24283843                            14                          12
## >7:24283548-24283843                          12                          11
## >78358469-78358619                             5                           7
## >7:128241036-1282413                           6                           5
## >6:31575210-31575467                          10                          11
## >31575210-31575467                            12                          11
## >24283796-24283936                             8                           8
## >2:25161598-25161833                          12                          12
## >7:24283796-24283936                          11                          13
## >17:78358469-7835861                          12                          12
##                      >8:22055623-22055743 4658_120BP
## >128241036-128241347                              14
## >25161598-25161833                                12
## >25168373-25168611                                15
## >2:25168373-25168611                              15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >6:31575210-31575467                              13
## >31575210-31575467                                11
## >24283796-24283936                                10
## >2:25161598-25161833                              11
## >7:24283796-24283936                              12
## >17:78358469-7835861                              12
##                      >18611255-18611340 1032_85BP >10:6307518-6307583 670_65BP
## >128241036-128241347                           17                           17
## >25161598-25161833                             14                           14
## >25168373-25168611                             16                           16
## >2:25168373-25168611                           17                           17
## >24283548-24283843                             14                           14
## >7:24283548-24283843                           14                           14
## >78358469-78358619                              8                            8
## >7:128241036-1282413                            7                            7
## >6:31575210-31575467                           13                           13
## >31575210-31575467                             10                           10
## >24283796-24283936                             12                           12
## >2:25161598-25161833                           10                           10
## >7:24283796-24283936                           12                           12
## >17:78358469-7835861                           10                           10
##                      >Y:12869910-12869975 675_65BP >5:865245-865502 1154_257BP
## >128241036-128241347                            17                          11
## >25161598-25161833                              14                          11
## >25168373-25168611                              16                          13
## >2:25168373-25168611                            17                          10
## >24283548-24283843                              14                          12
## >7:24283548-24283843                            14                          13
## >78358469-78358619                               8                          14
## >7:128241036-1282413                             7                          14
## >6:31575210-31575467                            13                          13
## >31575210-31575467                              10                          12
## >24283796-24283936                              12                          12
## >2:25161598-25161833                            10                          11
## >7:24283796-24283936                            12                          14
## >17:78358469-7835861                            10                          10
##                      >5:181195639-181195726 116_87BP
## >128241036-128241347                              14
## >25161598-25161833                                11
## >25168373-25168611                                14
## >2:25168373-25168611                              12
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >78358469-78358619                                16
## >7:128241036-1282413                              14
## >6:31575210-31575467                              15
## >31575210-31575467                                14
## >24283796-24283936                                14
## >2:25161598-25161833                               9
## >7:24283796-24283936                              12
## >17:78358469-7835861                              12
##                      >5:10649438-10649513 11895_75BP
## >128241036-128241347                              14
## >25161598-25161833                                15
## >25168373-25168611                                16
## >2:25168373-25168611                               9
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >78358469-78358619                                13
## >7:128241036-1282413                              13
## >6:31575210-31575467                              13
## >31575210-31575467                                14
## >24283796-24283936                                13
## >2:25161598-25161833                              12
## >7:24283796-24283936                              11
## >17:78358469-7835861                              13
##                      >8:37701095-37701196 243_101BP >4550782-4550844 206_62BP
## >128241036-128241347                             14                        12
## >25161598-25161833                               12                         9
## >25168373-25168611                               16                        11
## >2:25168373-25168611                              9                        11
## >24283548-24283843                               12                        12
## >7:24283548-24283843                             11                        10
## >78358469-78358619                               13                        15
## >7:128241036-1282413                             14                        17
## >6:31575210-31575467                             16                        17
## >31575210-31575467                               14                        14
## >24283796-24283936                               15                        14
## >2:25161598-25161833                             12                        15
## >7:24283796-24283936                             13                        14
## >17:78358469-7835861                             13                        17
##                      >37701095-37701196 243_101BP
## >128241036-128241347                           11
## >25161598-25161833                             10
## >25168373-25168611                             12
## >2:25168373-25168611                            8
## >24283548-24283843                             11
## >7:24283548-24283843                           11
## >78358469-78358619                             16
## >7:128241036-1282413                           16
## >6:31575210-31575467                           15
## >31575210-31575467                             13
## >24283796-24283936                             12
## >2:25161598-25161833                           14
## >7:24283796-24283936                           12
## >17:78358469-7835861                           13
##                      >5:131945721-131945786 875_65BP
## >128241036-128241347                              11
## >25161598-25161833                                10
## >25168373-25168611                                10
## >2:25168373-25168611                               8
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >78358469-78358619                                16
## >7:128241036-1282413                              16
## >6:31575210-31575467                              14
## >31575210-31575467                                16
## >24283796-24283936                                13
## >2:25161598-25161833                              13
## >7:24283796-24283936                              13
## >17:78358469-7835861                              14
##                      >10649438-10649513 11895_75BP >95526518-95526601 268_83BP
## >128241036-128241347                            12                          12
## >25161598-25161833                              10                          10
## >25168373-25168611                              14                          13
## >2:25168373-25168611                             8                           9
## >24283548-24283843                              10                          11
## >7:24283548-24283843                            12                          13
## >78358469-78358619                              16                          18
## >7:128241036-1282413                            15                          16
## >6:31575210-31575467                            15                          16
## >31575210-31575467                              13                          14
## >24283796-24283936                              14                          16
## >2:25161598-25161833                            11                          11
## >7:24283796-24283936                            14                          14
## >17:78358469-7835861                            12                          13
##                      >14989693-14989868 116_175BP >17:4550782-4550844 206_62BP
## >128241036-128241347                           12                           11
## >25161598-25161833                             10                           13
## >25168373-25168611                             12                           12
## >2:25168373-25168611                           11                           10
## >24283548-24283843                             10                           11
## >7:24283548-24283843                           12                           11
## >78358469-78358619                              7                           10
## >7:128241036-1282413                           11                           10
## >6:31575210-31575467                           10                           10
## >31575210-31575467                             13                           13
## >24283796-24283936                             13                           10
## >2:25161598-25161833                           10                           15
## >7:24283796-24283936                           11                           14
## >17:78358469-7835861                           13                           13
##                      >2:95526518-95526601 268_83BP
## >128241036-128241347                             9
## >25161598-25161833                              12
## >25168373-25168611                              13
## >2:25168373-25168611                             8
## >24283548-24283843                               8
## >7:24283548-24283843                             7
## >78358469-78358619                              13
## >7:128241036-1282413                            11
## >6:31575210-31575467                            10
## >31575210-31575467                              11
## >24283796-24283936                              10
## >2:25161598-25161833                            10
## >7:24283796-24283936                            13
## >17:78358469-7835861                            13
##                      >131945721-131945786 875_65BP
## >128241036-128241347                            11
## >25161598-25161833                              12
## >25168373-25168611                              13
## >2:25168373-25168611                            12
## >24283548-24283843                              10
## >7:24283548-24283843                             7
## >78358469-78358619                              11
## >7:128241036-1282413                            11
## >6:31575210-31575467                            10
## >31575210-31575467                               9
## >24283796-24283936                              10
## >2:25161598-25161833                            10
## >7:24283796-24283936                            14
## >17:78358469-7835861                            11
##                      >11:65726854-65726937 348_83BP
## >128241036-128241347                             11
## >25161598-25161833                               12
## >25168373-25168611                                8
## >2:25168373-25168611                              9
## >24283548-24283843                                9
## >7:24283548-24283843                              9
## >78358469-78358619                               13
## >7:128241036-1282413                             11
## >6:31575210-31575467                             15
## >31575210-31575467                                6
## >24283796-24283936                               10
## >2:25161598-25161833                             12
## >7:24283796-24283936                             13
## >17:78358469-7835861                             12
##                      >181195639-181195726 116_87BP
## >128241036-128241347                            13
## >25161598-25161833                               9
## >25168373-25168611                              12
## >2:25168373-25168611                            12
## >24283548-24283843                              11
## >7:24283548-24283843                            10
## >78358469-78358619                              14
## >7:128241036-1282413                            12
## >6:31575210-31575467                            14
## >31575210-31575467                               8
## >24283796-24283936                              12
## >2:25161598-25161833                             7
## >7:24283796-24283936                            11
## >17:78358469-7835861                            12
##                      >22055623-22055743 4658_120BP
## >128241036-128241347                             6
## >25161598-25161833                               9
## >25168373-25168611                               9
## >2:25168373-25168611                            10
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >6:31575210-31575467                             8
## >31575210-31575467                              11
## >24283796-24283936                              12
## >2:25161598-25161833                            11
## >7:24283796-24283936                            10
## >17:78358469-7835861                            13
##                      >1:58306257-58306325 156_68BP >65726854-65726937 348_83BP
## >128241036-128241347                             3                           9
## >25161598-25161833                               9                           9
## >25168373-25168611                              10                          10
## >2:25168373-25168611                            11                          11
## >24283548-24283843                              13                           9
## >7:24283548-24283843                            12                          10
## >78358469-78358619                              13                          12
## >7:128241036-1282413                            13                          15
## >6:31575210-31575467                            11                          12
## >31575210-31575467                              10                          11
## >24283796-24283936                              13                          11
## >2:25161598-25161833                            11                          11
## >7:24283796-24283936                             8                          12
## >17:78358469-7835861                            12                          12
##                      >16:14989693-14989868 116_175BP >865245-865502 1154_257BP
## >128241036-128241347                              11                         9
## >25161598-25161833                                10                        11
## >25168373-25168611                                 9                        10
## >2:25168373-25168611                              13                        12
## >24283548-24283843                                11                        10
## >7:24283548-24283843                              13                        12
## >78358469-78358619                                14                        15
## >7:128241036-1282413                              14                        15
## >6:31575210-31575467                              12                        13
## >31575210-31575467                                11                        14
## >24283796-24283936                                14                        13
## >2:25161598-25161833                              11                        10
## >7:24283796-24283936                              13                        12
## >17:78358469-7835861                              14                        14
##                      >1:18611255-18611340 1032_85BP >8288864-8288951 608_87BP
## >128241036-128241347                              4                         6
## >25161598-25161833                               11                        12
## >25168373-25168611                                8                        11
## >2:25168373-25168611                             10                        11
## >24283548-24283843                               11                        11
## >7:24283548-24283843                              9                         9
## >78358469-78358619                               16                        15
## >7:128241036-1282413                             15                        16
## >6:31575210-31575467                             12                        12
## >31575210-31575467                               12                        14
## >24283796-24283936                               13                        14
## >2:25161598-25161833                             15                        13
## >7:24283796-24283936                             12                        11
## >17:78358469-7835861                             14                        13
##                      >12869910-12869975 675_65BP >6307518-6307583 670_65BP
## >128241036-128241347                           7                         7
## >25161598-25161833                            12                        12
## >25168373-25168611                            11                        11
## >2:25168373-25168611                          10                        10
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >78358469-78358619                            14                        14
## >7:128241036-1282413                          16                        16
## >6:31575210-31575467                          10                        10
## >31575210-31575467                            13                        13
## >24283796-24283936                            13                        13
## >2:25161598-25161833                          15                        15
## >7:24283796-24283936                          12                        12
## >17:78358469-7835861                          11                        11
## 
## [[4]]$rowDendrogram
## 'dendrogram' with 2 branches and 30 members total, at height 22.36068 
## 
## [[4]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 35.49648 
## 
## [[4]]$breaks
##  [1]  3.0  3.3  3.6  3.9  4.2  4.5  4.8  5.1  5.4  5.7  6.0  6.3  6.6  6.9  7.2
## [16]  7.5  7.8  8.1  8.4  8.7  9.0  9.3  9.6  9.9 10.2 10.5 10.8 11.1 11.4 11.7
## [31] 12.0 12.3 12.6 12.9 13.2 13.5 13.8 14.1 14.4 14.7 15.0 15.3 15.6 15.9 16.2
## [46] 16.5 16.8 17.1 17.4 17.7 18.0
## 
## [[4]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[4]]$colorTable
##     low high   color
## 1   3.0  3.3 #FF0000
## 2   3.3  3.6 #FF0505
## 3   3.6  3.9 #FF0A0A
## 4   3.9  4.2 #FF0F0F
## 5   4.2  4.5 #FF1414
## 6   4.5  4.8 #FF1A1A
## 7   4.8  5.1 #FF1F1F
## 8   5.1  5.4 #FF2424
## 9   5.4  5.7 #FF2929
## 10  5.7  6.0 #FF2E2E
## 11  6.0  6.3 #FF3434
## 12  6.3  6.6 #FF3939
## 13  6.6  6.9 #FF3E3E
## 14  6.9  7.2 #FF4343
## 15  7.2  7.5 #FF4848
## 16  7.5  7.8 #FF4E4E
## 17  7.8  8.1 #FF5353
## 18  8.1  8.4 #FF5858
## 19  8.4  8.7 #FF5D5D
## 20  8.7  9.0 #FF6262
## 21  9.0  9.3 #FF6868
## 22  9.3  9.6 #FF6D6D
## 23  9.6  9.9 #FF7272
## 24  9.9 10.2 #FF7777
## 25 10.2 10.5 #FF7C7C
## 26 10.5 10.8 #FF8282
## 27 10.8 11.1 #FF8787
## 28 11.1 11.4 #FF8C8C
## 29 11.4 11.7 #FF9191
## 30 11.7 12.0 #FF9696
## 31 12.0 12.3 #FF9C9C
## 32 12.3 12.6 #FFA1A1
## 33 12.6 12.9 #FFA6A6
## 34 12.9 13.2 #FFABAB
## 35 13.2 13.5 #FFB0B0
## 36 13.5 13.8 #FFB6B6
## 37 13.8 14.1 #FFBBBB
## 38 14.1 14.4 #FFC0C0
## 39 14.4 14.7 #FFC5C5
## 40 14.7 15.0 #FFCACA
## 41 15.0 15.3 #FFD0D0
## 42 15.3 15.6 #FFD5D5
## 43 15.6 15.9 #FFDADA
## 44 15.9 16.2 #FFDFDF
## 45 16.2 16.5 #FFE4E4
## 46 16.5 16.8 #FFEAEA
## 47 16.8 17.1 #FFEFEF
## 48 17.1 17.4 #FFF4F4
## 49 17.4 17.7 #FFF9F9
## 50 17.7 18.0 #FFFFFF
## 
## [[4]]$layout
## [[4]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[4]]$layout$lhei
## [1] 1.5 4.0
## 
## [[4]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[5]]
## [[5]]$rowInd
##  [1] 15  4  8 13  2  9  6  5 10 18  7  3 12 14  1 17 11 16
## 
## [[5]]$colInd
##  [1] 14  7  2 10 13  1  8  3  9  5  4  6 11 12
## 
## [[5]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[5]]$carpet
##                      >221871203-221871265 1343_62BP
## >78358469-78358619                               13
## >7:128241036-1282413                             11
## >2:25161598-25161833                             11
## >24283796-24283936                               11
## >31575210-31575467                                8
## >17:78358469-7835861                             10
## >128241036-128241347                             12
## >2:25168373-25168611                             15
## >24283548-24283843                               14
## >7:24283548-24283843                             15
## >6:31575210-31575467                             12
## >7:24283796-24283936                              9
## >25161598-25161833                                9
## >25168373-25168611                               12
##                      >4:8288864-8288951 2343_87BP
## >78358469-78358619                              7
## >7:128241036-1282413                            5
## >2:25161598-25161833                           12
## >24283796-24283936                              8
## >31575210-31575467                             11
## >17:78358469-7835861                           12
## >128241036-128241347                           15
## >2:25168373-25168611                           15
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >6:31575210-31575467                           11
## >7:24283796-24283936                           13
## >25161598-25161833                             13
## >25168373-25168611                             14
##                      >8:22055623-22055743 2591_120BP
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25161598-25161833                              11
## >24283796-24283936                                10
## >31575210-31575467                                11
## >17:78358469-7835861                              12
## >128241036-128241347                              14
## >2:25168373-25168611                              15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >25161598-25161833                                12
## >25168373-25168611                                15
##                      >18611255-18611324 187_69BP >10:6307518-6307583 183_65BP
## >78358469-78358619                             8                            8
## >7:128241036-1282413                           7                            7
## >2:25161598-25161833                          10                           10
## >24283796-24283936                            12                           12
## >31575210-31575467                            10                           10
## >17:78358469-7835861                          10                           10
## >128241036-128241347                          17                           17
## >2:25168373-25168611                          17                           17
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >6:31575210-31575467                          13                           13
## >7:24283796-24283936                          12                           12
## >25161598-25161833                            14                           14
## >25168373-25168611                            16                           16
##                      >Y:12869910-12869975 184_65BP
## >78358469-78358619                               8
## >7:128241036-1282413                             7
## >2:25161598-25161833                            10
## >24283796-24283936                              12
## >31575210-31575467                              10
## >17:78358469-7835861                            10
## >128241036-128241347                            17
## >2:25168373-25168611                            17
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >6:31575210-31575467                            13
## >7:24283796-24283936                            12
## >25161598-25161833                              14
## >25168373-25168611                              16
##                      >5:10649438-10649513 9952_75BP >5:865245-865502 1563_257BP
## >78358469-78358619                               13                          14
## >7:128241036-1282413                             13                          14
## >2:25161598-25161833                             12                          11
## >24283796-24283936                               13                          12
## >31575210-31575467                               14                          12
## >17:78358469-7835861                             13                          10
## >128241036-128241347                             14                          11
## >2:25168373-25168611                              9                          10
## >24283548-24283843                               10                          12
## >7:24283548-24283843                             11                          13
## >6:31575210-31575467                             13                          13
## >7:24283796-24283936                             11                          14
## >25161598-25161833                               15                          11
## >25168373-25168611                               16                          13
##                      >10649438-10649513 9952_75BP >865245-865502 1563_257BP
## >78358469-78358619                             16                        15
## >7:128241036-1282413                           15                        15
## >2:25161598-25161833                           11                        10
## >24283796-24283936                             14                        13
## >31575210-31575467                             13                        14
## >17:78358469-7835861                           12                        14
## >128241036-128241347                           12                         9
## >2:25168373-25168611                            8                        12
## >24283548-24283843                             10                        10
## >7:24283548-24283843                           12                        12
## >6:31575210-31575467                           15                        13
## >7:24283796-24283936                           14                        12
## >25161598-25161833                             10                        11
## >25168373-25168611                             14                        10
##                      >5:131945721-131945786 637_65BP
## >78358469-78358619                                16
## >7:128241036-1282413                              16
## >2:25161598-25161833                              13
## >24283796-24283936                                13
## >31575210-31575467                                16
## >17:78358469-7835861                              14
## >128241036-128241347                              11
## >2:25168373-25168611                               8
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >6:31575210-31575467                              14
## >7:24283796-24283936                              13
## >25161598-25161833                                10
## >25168373-25168611                                10
##                      >2:221871203-221871265 1343_62BP
## >78358469-78358619                                  9
## >7:128241036-1282413                               11
## >2:25161598-25161833                               13
## >24283796-24283936                                  8
## >31575210-31575467                                  9
## >17:78358469-7835861                               12
## >128241036-128241347                               10
## >2:25168373-25168611                                9
## >24283548-24283843                                  4
## >7:24283548-24283843                               10
## >6:31575210-31575467                               11
## >7:24283796-24283936                               11
## >25161598-25161833                                 12
## >25168373-25168611                                  9
##                      >131945721-131945786 637_65BP
## >78358469-78358619                              11
## >7:128241036-1282413                            11
## >2:25161598-25161833                            10
## >24283796-24283936                              10
## >31575210-31575467                               9
## >17:78358469-7835861                            11
## >128241036-128241347                            11
## >2:25168373-25168611                            12
## >24283548-24283843                              10
## >7:24283548-24283843                             7
## >6:31575210-31575467                            10
## >7:24283796-24283936                            14
## >25161598-25161833                              12
## >25168373-25168611                              13
##                      >22055623-22055743 2591_120BP
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >2:25161598-25161833                            11
## >24283796-24283936                              12
## >31575210-31575467                              11
## >17:78358469-7835861                            13
## >128241036-128241347                             6
## >2:25168373-25168611                            10
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >6:31575210-31575467                             8
## >7:24283796-24283936                            10
## >25161598-25161833                               9
## >25168373-25168611                               9
##                      >1:18611255-18611324 187_69BP >8288864-8288951 2343_87BP
## >78358469-78358619                              16                         15
## >7:128241036-1282413                            15                         16
## >2:25161598-25161833                            15                         13
## >24283796-24283936                              13                         14
## >31575210-31575467                              12                         14
## >17:78358469-7835861                            14                         13
## >128241036-128241347                             4                          6
## >2:25168373-25168611                            10                         11
## >24283548-24283843                              11                         11
## >7:24283548-24283843                             9                          9
## >6:31575210-31575467                            12                         12
## >7:24283796-24283936                            12                         11
## >25161598-25161833                              11                         12
## >25168373-25168611                               8                         11
##                      >12869910-12869975 184_65BP >6307518-6307583 183_65BP
## >78358469-78358619                            14                        14
## >7:128241036-1282413                          16                        16
## >2:25161598-25161833                          15                        15
## >24283796-24283936                            13                        13
## >31575210-31575467                            13                        13
## >17:78358469-7835861                          11                        11
## >128241036-128241347                           7                         7
## >2:25168373-25168611                          10                        10
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >6:31575210-31575467                          10                        10
## >7:24283796-24283936                          12                        12
## >25161598-25161833                            12                        12
## >25168373-25168611                            11                        11
## 
## [[5]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 22.36068 
## 
## [[5]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 31.03224 
## 
## [[5]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[5]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[5]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[5]]$layout
## [[5]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[5]]$layout$lhei
## [1] 1.5 4.0
## 
## [[5]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[6]]
## [[6]]$rowInd
##  [1]  5  9 16  2 10  1 19 13 18 12 15 17 14  4  7  6 20  8  3 11
## 
## [[6]]$colInd
##  [1]  8 12  3 11  9  5  7 14  2  6  4  1 13 10
## 
## [[6]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[6]]$carpet
##                      >4:8288864-8288959 1995_95BP
## >128241036-128241347                           15
## >25168373-25168611                             14
## >2:25168373-25168611                           15
## >25161598-25161833                             13
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >7:128241036-1282413                            5
## >78358469-78358619                              7
## >2:25161598-25161833                           12
## >7:24283796-24283936                           13
## >6:31575210-31575467                           11
## >17:78358469-7835861                           12
## >31575210-31575467                             11
## >24283796-24283936                              8
##                      >8:22055623-22055743 4470_120BP
## >128241036-128241347                              14
## >25168373-25168611                                15
## >2:25168373-25168611                              15
## >25161598-25161833                                12
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >7:128241036-1282413                               7
## >78358469-78358619                                 7
## >2:25161598-25161833                              11
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >17:78358469-7835861                              12
## >31575210-31575467                                11
## >24283796-24283936                                10
##                      >18611255-18611324 268_69BP >10:6307518-6307583 263_65BP
## >128241036-128241347                          17                           17
## >25168373-25168611                            16                           16
## >2:25168373-25168611                          17                           17
## >25161598-25161833                            14                           14
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >7:128241036-1282413                           7                            7
## >78358469-78358619                             8                            8
## >2:25161598-25161833                          10                           10
## >7:24283796-24283936                          12                           12
## >6:31575210-31575467                          13                           13
## >17:78358469-7835861                          10                           10
## >31575210-31575467                            10                           10
## >24283796-24283936                            12                           12
##                      >Y:12869910-12869975 278_65BP
## >128241036-128241347                            17
## >25168373-25168611                              16
## >2:25168373-25168611                            17
## >25161598-25161833                              14
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >7:128241036-1282413                             7
## >78358469-78358619                               8
## >2:25161598-25161833                            10
## >7:24283796-24283936                            12
## >6:31575210-31575467                            13
## >17:78358469-7835861                            10
## >31575210-31575467                              10
## >24283796-24283936                              12
##                      >1:18611255-18611324 268_69BP >8288864-8288959 1995_95BP
## >128241036-128241347                             4                          6
## >25168373-25168611                               8                         10
## >2:25168373-25168611                            10                         11
## >25161598-25161833                              11                         12
## >24283548-24283843                              11                         10
## >7:24283548-24283843                             9                         11
## >7:128241036-1282413                            15                         16
## >78358469-78358619                              16                         15
## >2:25161598-25161833                            15                         14
## >7:24283796-24283936                            12                         13
## >6:31575210-31575467                            12                         13
## >17:78358469-7835861                            14                         12
## >31575210-31575467                              12                         12
## >24283796-24283936                              13                         13
##                      >12869910-12869975 278_65BP >6307518-6307583 263_65BP
## >128241036-128241347                           7                         7
## >25168373-25168611                            11                        11
## >2:25168373-25168611                          10                        10
## >25161598-25161833                            12                        12
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >7:128241036-1282413                          16                        16
## >78358469-78358619                            14                        14
## >2:25161598-25161833                          15                        15
## >7:24283796-24283936                          12                        12
## >6:31575210-31575467                          10                        10
## >17:78358469-7835861                          11                        11
## >31575210-31575467                            13                        13
## >24283796-24283936                            13                        13
##                      >1181147-1181217 222_70BP >14989690-14989868 107_178BP
## >128241036-128241347                        11                           12
## >25168373-25168611                          11                           12
## >2:25168373-25168611                        11                           11
## >25161598-25161833                          13                           10
## >24283548-24283843                          10                           10
## >7:24283548-24283843                        13                           12
## >7:128241036-1282413                        10                           11
## >78358469-78358619                          13                            7
## >2:25161598-25161833                         9                           10
## >7:24283796-24283936                        12                           11
## >6:31575210-31575467                        10                           10
## >17:78358469-7835861                         8                           13
## >31575210-31575467                          10                           13
## >24283796-24283936                          11                           13
##                      >22055623-22055743 4470_120BP
## >128241036-128241347                             6
## >25168373-25168611                               9
## >2:25168373-25168611                            10
## >25161598-25161833                               9
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >7:128241036-1282413                            13
## >78358469-78358619                              10
## >2:25161598-25161833                            11
## >7:24283796-24283936                            10
## >6:31575210-31575467                             8
## >17:78358469-7835861                            13
## >31575210-31575467                              11
## >24283796-24283936                              12
##                      >131945721-131945799 1567_78BP
## >128241036-128241347                             11
## >25168373-25168611                               11
## >2:25168373-25168611                             11
## >25161598-25161833                               10
## >24283548-24283843                               12
## >7:24283548-24283843                             10
## >7:128241036-1282413                             12
## >78358469-78358619                               12
## >2:25161598-25161833                             12
## >7:24283796-24283936                             10
## >6:31575210-31575467                             12
## >17:78358469-7835861                             11
## >31575210-31575467                               11
## >24283796-24283936                               10
##                      >16:14989690-14989868 107_178BP
## >128241036-128241347                               9
## >25168373-25168611                                10
## >2:25168373-25168611                              12
## >25161598-25161833                                 9
## >24283548-24283843                                12
## >7:24283548-24283843                              10
## >7:128241036-1282413                              11
## >78358469-78358619                                13
## >2:25161598-25161833                               9
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >17:78358469-7835861                              14
## >31575210-31575467                                10
## >24283796-24283936                                12
##                      >5:10649438-10649513 10509_75BP >5:865245-865502 793_257BP
## >128241036-128241347                              14                         11
## >25168373-25168611                                16                         13
## >2:25168373-25168611                               9                         10
## >25161598-25161833                                15                         11
## >24283548-24283843                                10                         12
## >7:24283548-24283843                              11                         13
## >7:128241036-1282413                              13                         14
## >78358469-78358619                                13                         14
## >2:25161598-25161833                              12                         11
## >7:24283796-24283936                              11                         14
## >6:31575210-31575467                              13                         13
## >17:78358469-7835861                              13                         10
## >31575210-31575467                                14                         12
## >24283796-24283936                                13                         12
##                      >865245-865502 793_257BP >5:131945721-131945799 1567_78BP
## >128241036-128241347                        9                               11
## >25168373-25168611                         10                               10
## >2:25168373-25168611                       12                                8
## >25161598-25161833                         11                               10
## >24283548-24283843                         10                               10
## >7:24283548-24283843                       12                               12
## >7:128241036-1282413                       15                               16
## >78358469-78358619                         15                               16
## >2:25161598-25161833                       10                               13
## >7:24283796-24283936                       12                               13
## >6:31575210-31575467                       13                               14
## >17:78358469-7835861                       14                               14
## >31575210-31575467                         14                               16
## >24283796-24283936                         13                               13
##                      >11:1181147-1181217 222_70BP >10649438-10649513 10509_75BP
## >128241036-128241347                           11                            12
## >25168373-25168611                             14                            14
## >2:25168373-25168611                            9                             8
## >25161598-25161833                             10                            10
## >24283548-24283843                             10                            10
## >7:24283548-24283843                           11                            12
## >7:128241036-1282413                           15                            15
## >78358469-78358619                             15                            16
## >2:25161598-25161833                           14                            11
## >7:24283796-24283936                           11                            14
## >6:31575210-31575467                           14                            15
## >17:78358469-7835861                           13                            12
## >31575210-31575467                             14                            13
## >24283796-24283936                             15                            14
## 
## [[6]]$rowDendrogram
## 'dendrogram' with 2 branches and 20 members total, at height 22.36068 
## 
## [[6]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 31.36877 
## 
## [[6]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[6]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[6]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[6]]$layout
## [[6]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[6]]$layout$lhei
## [1] 1.5 4.0
## 
## [[6]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[7]]
## [[7]]$rowInd
##  [1] 12 13  3  7 14  2  9  5  4 10 18  6 15  1 17  8 11 16
## 
## [[7]]$colInd
##  [1]  8  3 11 12 14  7  9  5  4  6  2  1 13 10
## 
## [[7]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[7]]$carpet
##                      >131945721-131945786 1053_65BP
## >128241036-128241347                             11
## >2:25168373-25168611                             12
## >25161598-25161833                               12
## >25168373-25168611                               13
## >78358469-78358619                               11
## >7:128241036-1282413                             11
## >24283548-24283843                               10
## >7:24283548-24283843                              7
## >6:31575210-31575467                             10
## >7:24283796-24283936                             14
## >2:25161598-25161833                             10
## >17:78358469-7835861                             11
## >31575210-31575467                                9
## >24283796-24283936                               10
##                      >153867168-153867235 102_67BP >4:8288864-8288951 309_87BP
## >128241036-128241347                            15                          15
## >2:25168373-25168611                            12                          15
## >25161598-25161833                              13                          13
## >25168373-25168611                              15                          14
## >78358469-78358619                              12                           7
## >7:128241036-1282413                            12                           5
## >24283548-24283843                              10                          12
## >7:24283548-24283843                             9                          11
## >6:31575210-31575467                            12                          11
## >7:24283796-24283936                            14                          13
## >2:25161598-25161833                             9                          12
## >17:78358469-7835861                             8                          12
## >31575210-31575467                              11                          11
## >24283796-24283936                              12                           8
##                      >8:22055623-22055743 4016_120BP
## >128241036-128241347                              14
## >2:25168373-25168611                              15
## >25161598-25161833                                12
## >25168373-25168611                                15
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
## >31575210-31575467                                11
## >24283796-24283936                                10
##                      >18611255-18611336 621_81BP >10:6307508-6307583 570_75BP
## >128241036-128241347                          17                           17
## >2:25168373-25168611                          17                           17
## >25161598-25161833                            14                           14
## >25168373-25168611                            16                           16
## >78358469-78358619                             8                            8
## >7:128241036-1282413                           7                            7
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >6:31575210-31575467                          13                           13
## >7:24283796-24283936                          12                           12
## >2:25161598-25161833                          10                           10
## >17:78358469-7835861                          10                           10
## >31575210-31575467                            10                           10
## >24283796-24283936                            12                           12
##                      >Y:12869910-12869975 411_65BP
## >128241036-128241347                            17
## >2:25168373-25168611                            17
## >25161598-25161833                              14
## >25168373-25168611                              16
## >78358469-78358619                               8
## >7:128241036-1282413                             7
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >6:31575210-31575467                            13
## >7:24283796-24283936                            12
## >2:25161598-25161833                            10
## >17:78358469-7835861                            10
## >31575210-31575467                              10
## >24283796-24283936                              12
##                      >5:10649438-10649513 11662_75BP >5:865245-865502 938_257BP
## >128241036-128241347                              14                         11
## >2:25168373-25168611                               9                         10
## >25161598-25161833                                15                         11
## >25168373-25168611                                16                         13
## >78358469-78358619                                13                         14
## >7:128241036-1282413                              13                         14
## >24283548-24283843                                10                         12
## >7:24283548-24283843                              11                         13
## >6:31575210-31575467                              13                         13
## >7:24283796-24283936                              11                         14
## >2:25161598-25161833                              12                         11
## >17:78358469-7835861                              13                         10
## >31575210-31575467                                14                         12
## >24283796-24283936                                13                         12
##                      >10649438-10649513 11662_75BP >865245-865502 938_257BP
## >128241036-128241347                            12                        9
## >2:25168373-25168611                             8                       12
## >25161598-25161833                              10                       11
## >25168373-25168611                              14                       10
## >78358469-78358619                              16                       15
## >7:128241036-1282413                            15                       15
## >24283548-24283843                              10                       10
## >7:24283548-24283843                            12                       12
## >6:31575210-31575467                            15                       13
## >7:24283796-24283936                            14                       12
## >2:25161598-25161833                            11                       10
## >17:78358469-7835861                            12                       14
## >31575210-31575467                              13                       14
## >24283796-24283936                              14                       13
##                      >5:131945721-131945786 1053_65BP
## >128241036-128241347                               11
## >2:25168373-25168611                                8
## >25161598-25161833                                 10
## >25168373-25168611                                 10
## >78358469-78358619                                 16
## >7:128241036-1282413                               16
## >24283548-24283843                                 10
## >7:24283548-24283843                               12
## >6:31575210-31575467                               14
## >7:24283796-24283936                               13
## >2:25161598-25161833                               13
## >17:78358469-7835861                               14
## >31575210-31575467                                 16
## >24283796-24283936                                 13
##                      >22055623-22055743 4016_120BP
## >128241036-128241347                             6
## >2:25168373-25168611                            10
## >25161598-25161833                               9
## >25168373-25168611                               9
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >6:31575210-31575467                             8
## >7:24283796-24283936                            10
## >2:25161598-25161833                            11
## >17:78358469-7835861                            13
## >31575210-31575467                              11
## >24283796-24283936                              12
##                      >1:18611255-18611336 621_81BP >8288864-8288951 309_87BP
## >128241036-128241347                             4                         6
## >2:25168373-25168611                            10                        11
## >25161598-25161833                              11                        12
## >25168373-25168611                               8                        11
## >78358469-78358619                              16                        15
## >7:128241036-1282413                            15                        16
## >24283548-24283843                              11                        11
## >7:24283548-24283843                             9                         9
## >6:31575210-31575467                            12                        12
## >7:24283796-24283936                            12                        11
## >2:25161598-25161833                            15                        13
## >17:78358469-7835861                            14                        13
## >31575210-31575467                              12                        14
## >24283796-24283936                              13                        14
##                      >X:153867168-153867235 102_67BP
## >128241036-128241347                               8
## >2:25168373-25168611                               9
## >25161598-25161833                                11
## >25168373-25168611                                10
## >78358469-78358619                                12
## >7:128241036-1282413                              13
## >24283548-24283843                                 8
## >7:24283548-24283843                              11
## >6:31575210-31575467                              12
## >7:24283796-24283936                              12
## >2:25161598-25161833                              12
## >17:78358469-7835861                              13
## >31575210-31575467                                12
## >24283796-24283936                                11
##                      >12869910-12869975 411_65BP >6307508-6307583 570_75BP
## >128241036-128241347                           7                         7
## >2:25168373-25168611                          10                        10
## >25161598-25161833                            12                        12
## >25168373-25168611                            11                        11
## >78358469-78358619                            14                        14
## >7:128241036-1282413                          16                        16
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >6:31575210-31575467                          10                        10
## >7:24283796-24283936                          12                        12
## >2:25161598-25161833                          15                        15
## >17:78358469-7835861                          11                        11
## >31575210-31575467                            13                        13
## >24283796-24283936                            13                        13
## 
## [[7]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 22.36068 
## 
## [[7]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 31.54362 
## 
## [[7]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[7]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[7]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[7]]$layout
## [[7]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[7]]$layout$lhei
## [1] 1.5 4.0
## 
## [[7]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[8]]
## [[8]]$rowInd
##  [1]  7 12  4  5  9  2 13 15  6 10 18  8 14 11  3 16  1 17
## 
## [[8]]$colInd
##  [1]  8  3  9  5 11 12 14  7  2  6  4  1 10 13
## 
## [[8]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[8]]$carpet
##                      >5:10649438-10649513 9805_75BP
## >128241036-128241347                             14
## >2:25168373-25168611                              9
## >24283548-24283843                               10
## >7:24283548-24283843                             11
## >25161598-25161833                               15
## >25168373-25168611                               16
## >78358469-78358619                               13
## >7:128241036-1282413                             13
## >2:25161598-25161833                             12
## >7:24283796-24283936                             11
## >6:31575210-31575467                             13
## >17:78358469-7835861                             13
## >24283796-24283936                               13
## >31575210-31575467                               14
##                      >14989690-14989869 180_179BP >17:4550782-4550844 300_62BP
## >128241036-128241347                           12                           11
## >2:25168373-25168611                           12                           10
## >24283548-24283843                             10                           11
## >7:24283548-24283843                           12                           11
## >25161598-25161833                             11                           13
## >25168373-25168611                             13                           12
## >78358469-78358619                              8                           10
## >7:128241036-1282413                           10                           10
## >2:25161598-25161833                           11                           15
## >7:24283796-24283936                           11                           14
## >6:31575210-31575467                           10                           10
## >17:78358469-7835861                           12                           13
## >24283796-24283936                             12                           10
## >31575210-31575467                             13                           13
##                      >4:8288864-8288951 3404_87BP
## >128241036-128241347                           15
## >2:25168373-25168611                           15
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >25161598-25161833                             13
## >25168373-25168611                             14
## >78358469-78358619                              7
## >7:128241036-1282413                            5
## >2:25161598-25161833                           12
## >7:24283796-24283936                           13
## >6:31575210-31575467                           11
## >17:78358469-7835861                           12
## >24283796-24283936                              8
## >31575210-31575467                             11
##                      >8:22055623-22055743 3942_120BP
## >128241036-128241347                              14
## >2:25168373-25168611                              15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >25161598-25161833                                12
## >25168373-25168611                                15
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25161598-25161833                              11
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >17:78358469-7835861                              12
## >24283796-24283936                                10
## >31575210-31575467                                11
##                      >10:6307508-6307583 421_75BP >18611255-18611336 726_81BP
## >128241036-128241347                           17                          17
## >2:25168373-25168611                           17                          17
## >24283548-24283843                             14                          14
## >7:24283548-24283843                           14                          14
## >25161598-25161833                             14                          14
## >25168373-25168611                             16                          16
## >78358469-78358619                              8                           8
## >7:128241036-1282413                            7                           7
## >2:25161598-25161833                           10                          10
## >7:24283796-24283936                           12                          12
## >6:31575210-31575467                           13                          13
## >17:78358469-7835861                           10                          10
## >24283796-24283936                             12                          12
## >31575210-31575467                             10                          10
##                      >4550782-4550844 300_62BP >5:865245-865502 2419_257BP
## >128241036-128241347                        12                          11
## >2:25168373-25168611                        11                          10
## >24283548-24283843                          12                          12
## >7:24283548-24283843                        10                          13
## >25161598-25161833                           9                          11
## >25168373-25168611                          11                          13
## >78358469-78358619                          15                          14
## >7:128241036-1282413                        17                          14
## >2:25161598-25161833                        15                          11
## >7:24283796-24283936                        14                          14
## >6:31575210-31575467                        17                          13
## >17:78358469-7835861                        17                          10
## >24283796-24283936                          14                          12
## >31575210-31575467                          14                          12
##                      >10649438-10649513 9805_75BP >865245-865502 2419_257BP
## >128241036-128241347                           12                         9
## >2:25168373-25168611                            8                        12
## >24283548-24283843                             10                        10
## >7:24283548-24283843                           12                        12
## >25161598-25161833                             10                        11
## >25168373-25168611                             14                        10
## >78358469-78358619                             16                        15
## >7:128241036-1282413                           15                        15
## >2:25161598-25161833                           11                        10
## >7:24283796-24283936                           14                        12
## >6:31575210-31575467                           15                        13
## >17:78358469-7835861                           12                        14
## >24283796-24283936                             14                        13
## >31575210-31575467                             13                        14
##                      >5:131945721-131945799 1392_78BP
## >128241036-128241347                               11
## >2:25168373-25168611                                8
## >24283548-24283843                                 10
## >7:24283548-24283843                               12
## >25161598-25161833                                 10
## >25168373-25168611                                 10
## >78358469-78358619                                 16
## >7:128241036-1282413                               16
## >2:25161598-25161833                               13
## >7:24283796-24283936                               13
## >6:31575210-31575467                               14
## >17:78358469-7835861                               14
## >24283796-24283936                                 13
## >31575210-31575467                                 16
##                      >22055623-22055743 3942_120BP
## >128241036-128241347                             6
## >2:25168373-25168611                            10
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >25161598-25161833                               9
## >25168373-25168611                               9
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >2:25161598-25161833                            11
## >7:24283796-24283936                            10
## >6:31575210-31575467                             8
## >17:78358469-7835861                            13
## >24283796-24283936                              12
## >31575210-31575467                              11
##                      >131945721-131945799 1392_78BP
## >128241036-128241347                             11
## >2:25168373-25168611                             11
## >24283548-24283843                               12
## >7:24283548-24283843                             10
## >25161598-25161833                               10
## >25168373-25168611                               11
## >78358469-78358619                               12
## >7:128241036-1282413                             12
## >2:25161598-25161833                             12
## >7:24283796-24283936                             10
## >6:31575210-31575467                             12
## >17:78358469-7835861                             11
## >24283796-24283936                               10
## >31575210-31575467                               11
##                      >16:14989690-14989869 180_179BP >6307508-6307583 421_75BP
## >128241036-128241347                               9                         7
## >2:25168373-25168611                              12                        10
## >24283548-24283843                                12                        10
## >7:24283548-24283843                              10                        12
## >25161598-25161833                                 9                        12
## >25168373-25168611                                10                        11
## >78358469-78358619                                13                        14
## >7:128241036-1282413                              11                        16
## >2:25161598-25161833                               9                        15
## >7:24283796-24283936                              12                        12
## >6:31575210-31575467                              13                        10
## >17:78358469-7835861                              14                        11
## >24283796-24283936                                12                        13
## >31575210-31575467                                10                        13
##                      >1:18611255-18611336 726_81BP >8288864-8288951 3404_87BP
## >128241036-128241347                             4                          6
## >2:25168373-25168611                            10                         11
## >24283548-24283843                              11                         11
## >7:24283548-24283843                             9                          9
## >25161598-25161833                              11                         12
## >25168373-25168611                               8                         11
## >78358469-78358619                              16                         15
## >7:128241036-1282413                            15                         16
## >2:25161598-25161833                            15                         13
## >7:24283796-24283936                            12                         11
## >6:31575210-31575467                            12                         12
## >17:78358469-7835861                            14                         13
## >24283796-24283936                              13                         14
## >31575210-31575467                              12                         14
## 
## [[8]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 22.36068 
## 
## [[8]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 28.5482 
## 
## [[8]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[8]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[8]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[8]]$layout
## [[8]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[8]]$layout$lhei
## [1] 1.5 4.0
## 
## [[8]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[9]]
## [[9]]$rowInd
##  [1]  2  7  1  5  8  9  4  3  6 10
## 
## [[9]]$colInd
##  [1] 14  7  9  5 10 13  2  1  3  8 11 12  4  6
## 
## [[9]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[9]]$carpet
##                      >5:865252-865490 133_238BP >131945721-131945786 510_65BP
## >78358469-78358619                           10                            11
## >7:128241036-1282413                         10                            11
## >24283548-24283843                            9                            10
## >7:24283548-24283843                         11                             7
## >24283796-24283936                           10                            10
## >31575210-31575467                            9                             9
## >2:25161598-25161833                         11                            10
## >17:78358469-7835861                         13                            11
## >2:25168373-25168611                          9                            12
## >128241036-128241347                         12                            11
## >25161598-25161833                           12                            12
## >25168373-25168611                           10                            13
## >6:31575210-31575467                         11                            10
## >7:24283796-24283936                         13                            14
##                      >4:8288864-8288951 3435_87BP
## >78358469-78358619                              7
## >7:128241036-1282413                            5
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >24283796-24283936                              8
## >31575210-31575467                             11
## >2:25161598-25161833                           12
## >17:78358469-7835861                           12
## >2:25168373-25168611                           15
## >128241036-128241347                           15
## >25161598-25161833                             13
## >25168373-25168611                             14
## >6:31575210-31575467                           11
## >7:24283796-24283936                           13
##                      >8:22055623-22055743 1924_120BP
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >24283796-24283936                                10
## >31575210-31575467                                11
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25161598-25161833                                12
## >25168373-25168611                                15
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
##                      >22055623-22055743 1924_120BP >8288864-8288951 3435_87BP
## >78358469-78358619                              10                         15
## >7:128241036-1282413                            13                         16
## >24283548-24283843                              11                         11
## >7:24283548-24283843                            13                          9
## >24283796-24283936                              12                         14
## >31575210-31575467                              11                         14
## >2:25161598-25161833                            11                         13
## >17:78358469-7835861                            13                         13
## >2:25168373-25168611                            10                         11
## >128241036-128241347                             6                          6
## >25161598-25161833                               9                         12
## >25168373-25168611                               9                         11
## >6:31575210-31575467                             8                         12
## >7:24283796-24283936                            10                         11
##                      >5:131945721-131945786 510_65BP
## >78358469-78358619                                16
## >7:128241036-1282413                              16
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >24283796-24283936                                13
## >31575210-31575467                                16
## >2:25161598-25161833                              13
## >17:78358469-7835861                              14
## >2:25168373-25168611                               8
## >128241036-128241347                              11
## >25161598-25161833                                10
## >25168373-25168611                                10
## >6:31575210-31575467                              14
## >7:24283796-24283936                              13
##                      >5:10649438-10649513 12054_75BP
## >78358469-78358619                                13
## >7:128241036-1282413                              13
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >24283796-24283936                                13
## >31575210-31575467                                14
## >2:25161598-25161833                              12
## >17:78358469-7835861                              13
## >2:25168373-25168611                               9
## >128241036-128241347                              14
## >25161598-25161833                                15
## >25168373-25168611                                16
## >6:31575210-31575467                              13
## >7:24283796-24283936                              11
##                      >10649438-10649513 12054_75BP >865252-865490 133_238BP
## >78358469-78358619                              16                       15
## >7:128241036-1282413                            15                       16
## >24283548-24283843                              10                       12
## >7:24283548-24283843                            12                       11
## >24283796-24283936                              14                       13
## >31575210-31575467                              13                       13
## >2:25161598-25161833                            11                       11
## >17:78358469-7835861                            12                       12
## >2:25168373-25168611                             8                        9
## >128241036-128241347                            12                       14
## >25161598-25161833                              10                       11
## >25168373-25168611                              14                       16
## >6:31575210-31575467                            15                       15
## >7:24283796-24283936                            14                       15
## 
## [[9]]$rowDendrogram
## 'dendrogram' with 2 branches and 10 members total, at height 19 
## 
## [[9]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 19.44222 
## 
## [[9]]$breaks
##  [1]  5.00  5.22  5.44  5.66  5.88  6.10  6.32  6.54  6.76  6.98  7.20  7.42
## [13]  7.64  7.86  8.08  8.30  8.52  8.74  8.96  9.18  9.40  9.62  9.84 10.06
## [25] 10.28 10.50 10.72 10.94 11.16 11.38 11.60 11.82 12.04 12.26 12.48 12.70
## [37] 12.92 13.14 13.36 13.58 13.80 14.02 14.24 14.46 14.68 14.90 15.12 15.34
## [49] 15.56 15.78 16.00
## 
## [[9]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[9]]$colorTable
##      low  high   color
## 1   5.00  5.22 #FF0000
## 2   5.22  5.44 #FF0505
## 3   5.44  5.66 #FF0A0A
## 4   5.66  5.88 #FF0F0F
## 5   5.88  6.10 #FF1414
## 6   6.10  6.32 #FF1A1A
## 7   6.32  6.54 #FF1F1F
## 8   6.54  6.76 #FF2424
## 9   6.76  6.98 #FF2929
## 10  6.98  7.20 #FF2E2E
## 11  7.20  7.42 #FF3434
## 12  7.42  7.64 #FF3939
## 13  7.64  7.86 #FF3E3E
## 14  7.86  8.08 #FF4343
## 15  8.08  8.30 #FF4848
## 16  8.30  8.52 #FF4E4E
## 17  8.52  8.74 #FF5353
## 18  8.74  8.96 #FF5858
## 19  8.96  9.18 #FF5D5D
## 20  9.18  9.40 #FF6262
## 21  9.40  9.62 #FF6868
## 22  9.62  9.84 #FF6D6D
## 23  9.84 10.06 #FF7272
## 24 10.06 10.28 #FF7777
## 25 10.28 10.50 #FF7C7C
## 26 10.50 10.72 #FF8282
## 27 10.72 10.94 #FF8787
## 28 10.94 11.16 #FF8C8C
## 29 11.16 11.38 #FF9191
## 30 11.38 11.60 #FF9696
## 31 11.60 11.82 #FF9C9C
## 32 11.82 12.04 #FFA1A1
## 33 12.04 12.26 #FFA6A6
## 34 12.26 12.48 #FFABAB
## 35 12.48 12.70 #FFB0B0
## 36 12.70 12.92 #FFB6B6
## 37 12.92 13.14 #FFBBBB
## 38 13.14 13.36 #FFC0C0
## 39 13.36 13.58 #FFC5C5
## 40 13.58 13.80 #FFCACA
## 41 13.80 14.02 #FFD0D0
## 42 14.02 14.24 #FFD5D5
## 43 14.24 14.46 #FFDADA
## 44 14.46 14.68 #FFDFDF
## 45 14.68 14.90 #FFE4E4
## 46 14.90 15.12 #FFEAEA
## 47 15.12 15.34 #FFEFEF
## 48 15.34 15.56 #FFF4F4
## 49 15.56 15.78 #FFF9F9
## 50 15.78 16.00 #FFFFFF
## 
## [[9]]$layout
## [[9]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[9]]$layout$lhei
## [1] 1.5 4.0
## 
## [[9]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[10]]
## [[10]]$rowInd
##  [1] 13  5  9 15  2 10  8 14  7  6 11  1 19 12 18 16  4 17  3 20
## 
## [[10]]$colInd
##  [1] 14  7  2 10 13  1  8  3 11 12  9  5  6  4
## 
## [[10]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[10]]$carpet
##                      >131945721-131945786 536_65BP >4:8288864-8288951 1958_87BP
## >78358469-78358619                              11                            7
## >7:128241036-1282413                            11                            5
## >2:25161598-25161833                            10                           12
## >24283796-24283936                              10                            8
## >31575210-31575467                               9                           11
## >17:78358469-7835861                            11                           12
## >128241036-128241347                            11                           15
## >2:25168373-25168611                            12                           15
## >25161598-25161833                              12                           13
## >25168373-25168611                              13                           14
## >24283548-24283843                              10                           12
## >7:24283548-24283843                             7                           11
## >7:24283796-24283936                            14                           13
## >6:31575210-31575467                            10                           11
##                      >8:22055623-22055743 2302_120BP
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25161598-25161833                              11
## >24283796-24283936                                10
## >31575210-31575467                                11
## >17:78358469-7835861                              12
## >128241036-128241347                              14
## >2:25168373-25168611                              15
## >25161598-25161833                                12
## >25168373-25168611                                15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
##                      >18611255-18611336 335_81BP >10:6307522-6307583 121_61BP
## >78358469-78358619                             8                            8
## >7:128241036-1282413                           7                            7
## >2:25161598-25161833                          10                           10
## >24283796-24283936                            12                           12
## >31575210-31575467                            10                           10
## >17:78358469-7835861                          10                           10
## >128241036-128241347                          17                           17
## >2:25168373-25168611                          17                           17
## >25161598-25161833                            14                           14
## >25168373-25168611                            16                           16
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >7:24283796-24283936                          12                           12
## >6:31575210-31575467                          13                           13
##                      >Y:12869910-12869975 127_65BP
## >78358469-78358619                               8
## >7:128241036-1282413                             7
## >2:25161598-25161833                            10
## >24283796-24283936                              12
## >31575210-31575467                              10
## >17:78358469-7835861                            10
## >128241036-128241347                            17
## >2:25168373-25168611                            17
## >25161598-25161833                              14
## >25168373-25168611                              16
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >7:24283796-24283936                            12
## >6:31575210-31575467                            13
##                      >5:131945721-131945786 536_65BP
## >78358469-78358619                                16
## >7:128241036-1282413                              16
## >2:25161598-25161833                              13
## >24283796-24283936                                13
## >31575210-31575467                                16
## >17:78358469-7835861                              14
## >128241036-128241347                              11
## >2:25168373-25168611                               8
## >25161598-25161833                                10
## >25168373-25168611                                10
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >7:24283796-24283936                              13
## >6:31575210-31575467                              14
##                      >14989629-14989930 302_301BP
## >78358469-78358619                             15
## >7:128241036-1282413                           17
## >2:25161598-25161833                           14
## >24283796-24283936                             15
## >31575210-31575467                             15
## >17:78358469-7835861                           16
## >128241036-128241347                           11
## >2:25168373-25168611                            8
## >25161598-25161833                             10
## >25168373-25168611                             15
## >24283548-24283843                             12
## >7:24283548-24283843                           12
## >7:24283796-24283936                           11
## >6:31575210-31575467                           15
##                      >5:10649438-10649513 6016_75BP >5:865245-865502 2675_257BP
## >78358469-78358619                               13                          14
## >7:128241036-1282413                             13                          14
## >2:25161598-25161833                             12                          11
## >24283796-24283936                               13                          12
## >31575210-31575467                               14                          12
## >17:78358469-7835861                             13                          10
## >128241036-128241347                             14                          11
## >2:25168373-25168611                              9                          10
## >25161598-25161833                               15                          11
## >25168373-25168611                               16                          13
## >24283548-24283843                               10                          12
## >7:24283548-24283843                             11                          13
## >7:24283796-24283936                             11                          14
## >6:31575210-31575467                             13                          13
##                      >10649438-10649513 6016_75BP >1:18611255-18611336 335_81BP
## >78358469-78358619                             16                            16
## >7:128241036-1282413                           15                            15
## >2:25161598-25161833                           11                            15
## >24283796-24283936                             14                            13
## >31575210-31575467                             13                            12
## >17:78358469-7835861                           12                            14
## >128241036-128241347                           12                             4
## >2:25168373-25168611                            8                            10
## >25161598-25161833                             10                            11
## >25168373-25168611                             14                             8
## >24283548-24283843                             10                            11
## >7:24283548-24283843                           12                             9
## >7:24283796-24283936                           14                            12
## >6:31575210-31575467                           15                            12
##                      >8288864-8288951 1958_87BP >12869910-12869975 127_65BP
## >78358469-78358619                           15                          14
## >7:128241036-1282413                         16                          16
## >2:25161598-25161833                         13                          15
## >24283796-24283936                           14                          13
## >31575210-31575467                           14                          13
## >17:78358469-7835861                         13                          11
## >128241036-128241347                          6                           7
## >2:25168373-25168611                         11                          10
## >25161598-25161833                           12                          12
## >25168373-25168611                           11                          11
## >24283548-24283843                           11                          10
## >7:24283548-24283843                          9                          12
## >7:24283796-24283936                         11                          12
## >6:31575210-31575467                         12                          10
##                      >6307522-6307583 121_61BP >22055623-22055743 2302_120BP
## >78358469-78358619                          14                            10
## >7:128241036-1282413                        16                            13
## >2:25161598-25161833                        15                            11
## >24283796-24283936                          13                            12
## >31575210-31575467                          13                            11
## >17:78358469-7835861                        11                            13
## >128241036-128241347                         7                             6
## >2:25168373-25168611                        10                            10
## >25161598-25161833                          12                             9
## >25168373-25168611                          11                             9
## >24283548-24283843                          10                            11
## >7:24283548-24283843                        12                            13
## >7:24283796-24283936                        12                            10
## >6:31575210-31575467                        10                             8
##                      >22:29788944-29789092 197_148BP
## >78358469-78358619                                12
## >7:128241036-1282413                              14
## >2:25161598-25161833                              11
## >24283796-24283936                                13
## >31575210-31575467                                11
## >17:78358469-7835861                              12
## >128241036-128241347                              11
## >2:25168373-25168611                              11
## >25161598-25161833                                 8
## >25168373-25168611                                 9
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >7:24283796-24283936                              10
## >6:31575210-31575467                              14
##                      >29788944-29789092 197_148BP
## >78358469-78358619                             11
## >7:128241036-1282413                           13
## >2:25161598-25161833                           15
## >24283796-24283936                             11
## >31575210-31575467                             11
## >17:78358469-7835861                           13
## >128241036-128241347                           10
## >2:25168373-25168611                           11
## >25161598-25161833                             10
## >25168373-25168611                              8
## >24283548-24283843                             11
## >7:24283548-24283843                           11
## >7:24283796-24283936                           12
## >6:31575210-31575467                           13
##                      >16:14989629-14989930 302_301BP >865245-865502 2675_257BP
## >78358469-78358619                                14                        15
## >7:128241036-1282413                              14                        15
## >2:25161598-25161833                              12                        10
## >24283796-24283936                                14                        13
## >31575210-31575467                                13                        14
## >17:78358469-7835861                              14                        14
## >128241036-128241347                               7                         9
## >2:25168373-25168611                              12                        12
## >25161598-25161833                                10                        11
## >25168373-25168611                                 9                        10
## >24283548-24283843                                10                        10
## >7:24283548-24283843                              12                        12
## >7:24283796-24283936                              13                        12
## >6:31575210-31575467                              12                        13
## 
## [[10]]$rowDendrogram
## 'dendrogram' with 2 branches and 20 members total, at height 22.36068 
## 
## [[10]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 32.61901 
## 
## [[10]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[10]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[10]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[10]]$layout
## [[10]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[10]]$layout$lhei
## [1] 1.5 4.0
## 
## [[10]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[11]]
## [[11]]$rowInd
##  [1]  9  8 12 22 17  1 21 20 10 16  2  5  4  3 15 19  7 11 18 14  6 13
## 
## [[11]]$colInd
##  [1]  3  9  5 11  8 12 14  7 10 13  4  6  2  1
## 
## [[11]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[11]]$carpet
##                      >5:10649438-10649513 11258_75BP
## >2:25168373-25168611                               9
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >25161598-25161833                                15
## >128241036-128241347                              14
## >25168373-25168611                                16
## >78358469-78358619                                13
## >7:128241036-1282413                              13
## >24283796-24283936                                13
## >31575210-31575467                                14
## >6:31575210-31575467                              13
## >7:24283796-24283936                              11
## >2:25161598-25161833                              12
## >17:78358469-7835861                              13
##                      >5:865245-865502 3139_257BP >10649438-10649513 11258_75BP
## >2:25168373-25168611                          10                             8
## >24283548-24283843                            12                            10
## >7:24283548-24283843                          13                            12
## >25161598-25161833                            11                            10
## >128241036-128241347                          11                            12
## >25168373-25168611                            13                            14
## >78358469-78358619                            14                            16
## >7:128241036-1282413                          14                            15
## >24283796-24283936                            12                            14
## >31575210-31575467                            12                            13
## >6:31575210-31575467                          13                            15
## >7:24283796-24283936                          14                            14
## >2:25161598-25161833                          11                            11
## >17:78358469-7835861                          10                            12
##                      >95526518-95526601 111_83BP >4550782-4550844 138_62BP
## >2:25168373-25168611                           9                        11
## >24283548-24283843                            11                        12
## >7:24283548-24283843                          13                        10
## >25161598-25161833                            10                         9
## >128241036-128241347                          12                        12
## >25168373-25168611                            13                        11
## >78358469-78358619                            18                        15
## >7:128241036-1282413                          16                        17
## >24283796-24283936                            16                        14
## >31575210-31575467                            14                        14
## >6:31575210-31575467                          16                        17
## >7:24283796-24283936                          14                        14
## >2:25161598-25161833                          11                        15
## >17:78358469-7835861                          13                        17
##                      >11:115173455-115173532 313_77BP >865245-865502 3139_257BP
## >2:25168373-25168611                               11                        12
## >24283548-24283843                                 11                        10
## >7:24283548-24283843                                9                        12
## >25161598-25161833                                  9                        11
## >128241036-128241347                                7                         9
## >25168373-25168611                                  9                        10
## >78358469-78358619                                 13                        15
## >7:128241036-1282413                               16                        15
## >24283796-24283936                                 13                        13
## >31575210-31575467                                 14                        14
## >6:31575210-31575467                               14                        13
## >7:24283796-24283936                               15                        12
## >2:25161598-25161833                               13                        10
## >17:78358469-7835861                               15                        14
##                      >8288864-8288955 4024_91BP
## >2:25168373-25168611                          9
## >24283548-24283843                            9
## >7:24283548-24283843                         10
## >25161598-25161833                           10
## >128241036-128241347                          8
## >25168373-25168611                            9
## >78358469-78358619                           16
## >7:128241036-1282413                         16
## >24283796-24283936                           14
## >31575210-31575467                           13
## >6:31575210-31575467                         13
## >7:24283796-24283936                         13
## >2:25161598-25161833                         13
## >17:78358469-7835861                         13
##                      >5:131945721-131945786 1376_65BP
## >2:25168373-25168611                                8
## >24283548-24283843                                 10
## >7:24283548-24283843                               12
## >25161598-25161833                                 10
## >128241036-128241347                               11
## >25168373-25168611                                 10
## >78358469-78358619                                 16
## >7:128241036-1282413                               16
## >24283796-24283936                                 13
## >31575210-31575467                                 16
## >6:31575210-31575467                               14
## >7:24283796-24283936                               13
## >2:25161598-25161833                               13
## >17:78358469-7835861                               14
##                      >22055623-22055743 4129_120BP
## >2:25168373-25168611                            10
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >25161598-25161833                               9
## >128241036-128241347                             6
## >25168373-25168611                               9
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >24283796-24283936                              12
## >31575210-31575467                              11
## >6:31575210-31575467                             8
## >7:24283796-24283936                            10
## >2:25161598-25161833                            11
## >17:78358469-7835861                            13
##                      >13:69077731-69077797 210_66BP
## >2:25168373-25168611                             14
## >24283548-24283843                               11
## >7:24283548-24283843                             12
## >25161598-25161833                               11
## >128241036-128241347                             11
## >25168373-25168611                               10
## >78358469-78358619                               10
## >7:128241036-1282413                             11
## >24283796-24283936                               10
## >31575210-31575467                                9
## >6:31575210-31575467                             10
## >7:24283796-24283936                             13
## >2:25161598-25161833                             14
## >17:78358469-7835861                             14
##                      >17:4550782-4550844 138_62BP
## >2:25168373-25168611                           10
## >24283548-24283843                             11
## >7:24283548-24283843                           11
## >25161598-25161833                             13
## >128241036-128241347                           11
## >25168373-25168611                             12
## >78358469-78358619                             10
## >7:128241036-1282413                           10
## >24283796-24283936                             10
## >31575210-31575467                             13
## >6:31575210-31575467                           10
## >7:24283796-24283936                           14
## >2:25161598-25161833                           15
## >17:78358469-7835861                           13
##                      >16:66767740-66767838 201_98BP
## >2:25168373-25168611                             12
## >24283548-24283843                                8
## >7:24283548-24283843                             11
## >25161598-25161833                               12
## >128241036-128241347                             12
## >25168373-25168611                               11
## >78358469-78358619                                6
## >7:128241036-1282413                             11
## >24283796-24283936                               11
## >31575210-31575467                                9
## >6:31575210-31575467                             11
## >7:24283796-24283936                              9
## >2:25161598-25161833                             12
## >17:78358469-7835861                             13
##                      >16:14989689-14989870 197_181BP
## >2:25168373-25168611                              13
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >25161598-25161833                                10
## >128241036-128241347                               9
## >25168373-25168611                                10
## >78358469-78358619                                11
## >7:128241036-1282413                              10
## >24283796-24283936                                10
## >31575210-31575467                                12
## >6:31575210-31575467                              12
## >7:24283796-24283936                              11
## >2:25161598-25161833                              10
## >17:78358469-7835861                              12
##                      >14989689-14989870 197_181BP >69077731-69077797 210_66BP
## >2:25168373-25168611                           13                          15
## >24283548-24283843                             10                          12
## >7:24283548-24283843                           11                          15
## >25161598-25161833                              9                          12
## >128241036-128241347                           13                          14
## >25168373-25168611                             12                          13
## >78358469-78358619                              9                           9
## >7:128241036-1282413                           10                          10
## >24283796-24283936                             13                          11
## >31575210-31575467                             11                           9
## >6:31575210-31575467                           11                          10
## >7:24283796-24283936                           10                          10
## >2:25161598-25161833                           10                          12
## >17:78358469-7835861                           13                           9
##                      >4:8288864-8288955 4024_91BP
## >2:25168373-25168611                           15
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >25161598-25161833                             13
## >128241036-128241347                           15
## >25168373-25168611                             14
## >78358469-78358619                              7
## >7:128241036-1282413                            5
## >24283796-24283936                              8
## >31575210-31575467                             11
## >6:31575210-31575467                           11
## >7:24283796-24283936                           13
## >2:25161598-25161833                           12
## >17:78358469-7835861                           12
##                      >8:22055623-22055743 4129_120BP
## >2:25168373-25168611                              15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >25161598-25161833                                12
## >128241036-128241347                              14
## >25168373-25168611                                15
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >24283796-24283936                                10
## >31575210-31575467                                11
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
##                      >66767740-66767838 201_98BP >131945721-131945786 1376_65BP
## >2:25168373-25168611                          11                             12
## >24283548-24283843                             8                             10
## >7:24283548-24283843                          10                              7
## >25161598-25161833                            14                             12
## >128241036-128241347                          13                             11
## >25168373-25168611                            14                             13
## >78358469-78358619                            14                             11
## >7:128241036-1282413                           8                             11
## >24283796-24283936                             9                             10
## >31575210-31575467                            11                              9
## >6:31575210-31575467                          13                             10
## >7:24283796-24283936                          12                             14
## >2:25161598-25161833                          11                             10
## >17:78358469-7835861                          10                             11
##                      >2:95526518-95526601 111_83BP
## >2:25168373-25168611                             8
## >24283548-24283843                               8
## >7:24283548-24283843                             7
## >25161598-25161833                              12
## >128241036-128241347                             9
## >25168373-25168611                              13
## >78358469-78358619                              13
## >7:128241036-1282413                            11
## >24283796-24283936                              10
## >31575210-31575467                              11
## >6:31575210-31575467                            10
## >7:24283796-24283936                            13
## >2:25161598-25161833                            10
## >17:78358469-7835861                            13
##                      >115173455-115173532 313_77BP
## >2:25168373-25168611                             8
## >24283548-24283843                               9
## >7:24283548-24283843                             9
## >25161598-25161833                              12
## >128241036-128241347                            11
## >25168373-25168611                              12
## >78358469-78358619                              12
## >7:128241036-1282413                            13
## >24283796-24283936                              11
## >31575210-31575467                              12
## >6:31575210-31575467                            11
## >7:24283796-24283936                            11
## >2:25161598-25161833                            12
## >17:78358469-7835861                            12
## 
## [[11]]$rowDendrogram
## 'dendrogram' with 2 branches and 22 members total, at height 20.07486 
## 
## [[11]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 24.61707 
## 
## [[11]]$breaks
##  [1]  5.00  5.26  5.52  5.78  6.04  6.30  6.56  6.82  7.08  7.34  7.60  7.86
## [13]  8.12  8.38  8.64  8.90  9.16  9.42  9.68  9.94 10.20 10.46 10.72 10.98
## [25] 11.24 11.50 11.76 12.02 12.28 12.54 12.80 13.06 13.32 13.58 13.84 14.10
## [37] 14.36 14.62 14.88 15.14 15.40 15.66 15.92 16.18 16.44 16.70 16.96 17.22
## [49] 17.48 17.74 18.00
## 
## [[11]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[11]]$colorTable
##      low  high   color
## 1   5.00  5.26 #FF0000
## 2   5.26  5.52 #FF0505
## 3   5.52  5.78 #FF0A0A
## 4   5.78  6.04 #FF0F0F
## 5   6.04  6.30 #FF1414
## 6   6.30  6.56 #FF1A1A
## 7   6.56  6.82 #FF1F1F
## 8   6.82  7.08 #FF2424
## 9   7.08  7.34 #FF2929
## 10  7.34  7.60 #FF2E2E
## 11  7.60  7.86 #FF3434
## 12  7.86  8.12 #FF3939
## 13  8.12  8.38 #FF3E3E
## 14  8.38  8.64 #FF4343
## 15  8.64  8.90 #FF4848
## 16  8.90  9.16 #FF4E4E
## 17  9.16  9.42 #FF5353
## 18  9.42  9.68 #FF5858
## 19  9.68  9.94 #FF5D5D
## 20  9.94 10.20 #FF6262
## 21 10.20 10.46 #FF6868
## 22 10.46 10.72 #FF6D6D
## 23 10.72 10.98 #FF7272
## 24 10.98 11.24 #FF7777
## 25 11.24 11.50 #FF7C7C
## 26 11.50 11.76 #FF8282
## 27 11.76 12.02 #FF8787
## 28 12.02 12.28 #FF8C8C
## 29 12.28 12.54 #FF9191
## 30 12.54 12.80 #FF9696
## 31 12.80 13.06 #FF9C9C
## 32 13.06 13.32 #FFA1A1
## 33 13.32 13.58 #FFA6A6
## 34 13.58 13.84 #FFABAB
## 35 13.84 14.10 #FFB0B0
## 36 14.10 14.36 #FFB6B6
## 37 14.36 14.62 #FFBBBB
## 38 14.62 14.88 #FFC0C0
## 39 14.88 15.14 #FFC5C5
## 40 15.14 15.40 #FFCACA
## 41 15.40 15.66 #FFD0D0
## 42 15.66 15.92 #FFD5D5
## 43 15.92 16.18 #FFDADA
## 44 16.18 16.44 #FFDFDF
## 45 16.44 16.70 #FFE4E4
## 46 16.70 16.96 #FFEAEA
## 47 16.96 17.22 #FFEFEF
## 48 17.22 17.48 #FFF4F4
## 49 17.48 17.74 #FFF9F9
## 50 17.74 18.00 #FFFFFF
## 
## [[11]]$layout
## [[11]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[11]]$layout$lhei
## [1] 1.5 4.0
## 
## [[11]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[12]]
## [[12]]$rowInd
##  [1]  4 13  6 10 19  2 12 20 16 11  5 17  1 23  3 15 21 22  8 24  9  7 18 14
## 
## [[12]]$colInd
##  [1]  8  9  5  3 11 12  7 14  6  4  2  1 10 13
## 
## [[12]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[12]]$carpet
##                      >12:7913634-7913754 229_120BP
## >128241036-128241347                            15
## >24283548-24283843                              11
## >7:24283548-24283843                            10
## >2:25168373-25168611                            14
## >25161598-25161833                              15
## >25168373-25168611                              13
## >7:128241036-1282413                            10
## >78358469-78358619                              10
## >7:24283796-24283936                            15
## >6:31575210-31575467                            13
## >2:25161598-25161833                            14
## >17:78358469-7835861                            10
## >24283796-24283936                              10
## >31575210-31575467                              11
##                      >100122122-100122193 203_71BP >4:8288864-8288951 418_87BP
## >128241036-128241347                            16                          15
## >24283548-24283843                              12                          12
## >7:24283548-24283843                            12                          11
## >2:25168373-25168611                            16                          15
## >25161598-25161833                              16                          13
## >25168373-25168611                              15                          14
## >7:128241036-1282413                             7                           5
## >78358469-78358619                              11                           7
## >7:24283796-24283936                            15                          13
## >6:31575210-31575467                            14                          11
## >2:25161598-25161833                            12                          12
## >17:78358469-7835861                            10                          12
## >24283796-24283936                              11                           8
## >31575210-31575467                              12                          11
##                      >8:22055623-22055743 4618_120BP
## >128241036-128241347                              14
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >2:25168373-25168611                              15
## >25161598-25161833                                12
## >25168373-25168611                                15
## >7:128241036-1282413                               7
## >78358469-78358619                                 7
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
## >24283796-24283936                                10
## >31575210-31575467                                11
##                      >18611255-18611336 555_81BP >10:6307518-6307583 399_65BP
## >128241036-128241347                          17                           17
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >2:25168373-25168611                          17                           17
## >25161598-25161833                            14                           14
## >25168373-25168611                            16                           16
## >7:128241036-1282413                           7                            7
## >78358469-78358619                             8                            8
## >7:24283796-24283936                          12                           12
## >6:31575210-31575467                          13                           13
## >2:25161598-25161833                          10                           10
## >17:78358469-7835861                          10                           10
## >24283796-24283936                            12                           12
## >31575210-31575467                            10                           10
##                      >Y:12869905-12869975 508_70BP
## >128241036-128241347                            17
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >2:25168373-25168611                            17
## >25161598-25161833                              14
## >25168373-25168611                              16
## >7:128241036-1282413                             7
## >78358469-78358619                               8
## >7:24283796-24283936                            12
## >6:31575210-31575467                            13
## >2:25161598-25161833                            10
## >17:78358469-7835861                            10
## >24283796-24283936                              12
## >31575210-31575467                              10
##                      >22055623-22055743 4618_120BP
## >128241036-128241347                             6
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >2:25168373-25168611                            10
## >25161598-25161833                               9
## >25168373-25168611                               9
## >7:128241036-1282413                            13
## >78358469-78358619                              10
## >7:24283796-24283936                            10
## >6:31575210-31575467                             8
## >2:25161598-25161833                            11
## >17:78358469-7835861                            13
## >24283796-24283936                              12
## >31575210-31575467                              11
##                      >129284232-129284318 533_86BP
## >128241036-128241347                            11
## >24283548-24283843                              13
## >7:24283548-24283843                            16
## >2:25168373-25168611                            14
## >25161598-25161833                              11
## >25168373-25168611                              11
## >7:128241036-1282413                            14
## >78358469-78358619                               9
## >7:24283796-24283936                             9
## >6:31575210-31575467                             8
## >2:25161598-25161833                            13
## >17:78358469-7835861                            14
## >24283796-24283936                              13
## >31575210-31575467                              11
##                      >9:129284232-129284318 533_86BP
## >128241036-128241347                              12
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >2:25168373-25168611                              14
## >25161598-25161833                                11
## >25168373-25168611                                12
## >7:128241036-1282413                              10
## >78358469-78358619                                 9
## >7:24283796-24283936                              11
## >6:31575210-31575467                              15
## >2:25161598-25161833                              11
## >17:78358469-7835861                              11
## >24283796-24283936                                10
## >31575210-31575467                                 8
##                      >3:14555195-14555262 136_67BP
## >128241036-128241347                            11
## >24283548-24283843                               8
## >7:24283548-24283843                            10
## >2:25168373-25168611                            13
## >25161598-25161833                               9
## >25168373-25168611                              12
## >7:128241036-1282413                            11
## >78358469-78358619                              10
## >7:24283796-24283936                             8
## >6:31575210-31575467                            13
## >2:25161598-25161833                            12
## >17:78358469-7835861                            13
## >24283796-24283936                              10
## >31575210-31575467                              10
##                      >131945721-131945799 2815_78BP
## >128241036-128241347                             11
## >24283548-24283843                               12
## >7:24283548-24283843                             10
## >2:25168373-25168611                             11
## >25161598-25161833                               10
## >25168373-25168611                               11
## >7:128241036-1282413                             12
## >78358469-78358619                               12
## >7:24283796-24283936                             10
## >6:31575210-31575467                             12
## >2:25161598-25161833                             12
## >17:78358469-7835861                             11
## >24283796-24283936                               10
## >31575210-31575467                               11
##                      >1:18611255-18611336 555_81BP >8288864-8288951 418_87BP
## >128241036-128241347                             4                         6
## >24283548-24283843                              11                        11
## >7:24283548-24283843                             9                         9
## >2:25168373-25168611                            10                        11
## >25161598-25161833                              11                        12
## >25168373-25168611                               8                        11
## >7:128241036-1282413                            15                        16
## >78358469-78358619                              16                        15
## >7:24283796-24283936                            12                        11
## >6:31575210-31575467                            12                        12
## >2:25161598-25161833                            15                        13
## >17:78358469-7835861                            14                        13
## >24283796-24283936                              13                        14
## >31575210-31575467                              12                        14
##                      >10:100122122-100122193 203_71BP
## >128241036-128241347                                7
## >24283548-24283843                                 11
## >7:24283548-24283843                               11
## >2:25168373-25168611                                9
## >25161598-25161833                                 12
## >25168373-25168611                                 11
## >7:128241036-1282413                               15
## >78358469-78358619                                 16
## >7:24283796-24283936                               11
## >6:31575210-31575467                               10
## >2:25161598-25161833                               15
## >17:78358469-7835861                               12
## >24283796-24283936                                 14
## >31575210-31575467                                 13
##                      >12869905-12869975 508_70BP >6307518-6307583 399_65BP
## >128241036-128241347                           7                         7
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >2:25168373-25168611                          10                        10
## >25161598-25161833                            12                        12
## >25168373-25168611                            11                        11
## >7:128241036-1282413                          16                        16
## >78358469-78358619                            14                        14
## >7:24283796-24283936                          12                        12
## >6:31575210-31575467                          10                        10
## >2:25161598-25161833                          15                        15
## >17:78358469-7835861                          11                        11
## >24283796-24283936                            13                        13
## >31575210-31575467                            13                        13
##                      >7913634-7913754 229_120BP >5:10649438-10649513 12873_75BP
## >128241036-128241347                         12                              14
## >24283548-24283843                            9                              10
## >7:24283548-24283843                          9                              11
## >2:25168373-25168611                          9                               9
## >25161598-25161833                           13                              15
## >25168373-25168611                           13                              16
## >7:128241036-1282413                          9                              13
## >78358469-78358619                           13                              13
## >7:24283796-24283936                         12                              11
## >6:31575210-31575467                         14                              13
## >2:25161598-25161833                         13                              12
## >17:78358469-7835861                         12                              13
## >24283796-24283936                            9                              13
## >31575210-31575467                           11                              14
##                      >865245-865502 1057_257BP >5:131945721-131945799 2815_78BP
## >128241036-128241347                         9                               11
## >24283548-24283843                          10                               10
## >7:24283548-24283843                        12                               12
## >2:25168373-25168611                        12                                8
## >25161598-25161833                          11                               10
## >25168373-25168611                          10                               10
## >7:128241036-1282413                        15                               16
## >78358469-78358619                          15                               16
## >7:24283796-24283936                        12                               13
## >6:31575210-31575467                        13                               14
## >2:25161598-25161833                        10                               13
## >17:78358469-7835861                        14                               14
## >24283796-24283936                          13                               13
## >31575210-31575467                          14                               16
##                      >5:865245-865502 1057_257BP >14555195-14555262 136_67BP
## >128241036-128241347                          11                          13
## >24283548-24283843                            12                          10
## >7:24283548-24283843                          13                          11
## >2:25168373-25168611                          10                           9
## >25161598-25161833                            11                          10
## >25168373-25168611                            13                          13
## >7:128241036-1282413                          14                          14
## >78358469-78358619                            14                          14
## >7:24283796-24283936                          14                          13
## >6:31575210-31575467                          13                          16
## >2:25161598-25161833                          11                          11
## >17:78358469-7835861                          10                          12
## >24283796-24283936                            12                          13
## >31575210-31575467                            12                          13
##                      >10649438-10649513 12873_75BP
## >128241036-128241347                            12
## >24283548-24283843                              10
## >7:24283548-24283843                            12
## >2:25168373-25168611                             8
## >25161598-25161833                              10
## >25168373-25168611                              14
## >7:128241036-1282413                            15
## >78358469-78358619                              16
## >7:24283796-24283936                            14
## >6:31575210-31575467                            15
## >2:25161598-25161833                            11
## >17:78358469-7835861                            12
## >24283796-24283936                              14
## >31575210-31575467                              13
## 
## [[12]]$rowDendrogram
## 'dendrogram' with 2 branches and 24 members total, at height 22.36068 
## 
## [[12]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 33.98529 
## 
## [[12]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[12]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[12]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[12]]$layout
## [[12]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[12]]$layout$lhei
## [1] 1.5 4.0
## 
## [[12]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[13]]
## [[13]]$rowInd
##  [1]  9  3  7 13  5 10  6  8 11  2  4  1 12 14
## 
## [[13]]$colInd
##  [1]  8 12  3 11  9  5 14  7  6  4 10  2 13  1
## 
## [[13]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[13]]$carpet
##                      >131945721-131945786 143_65BP
## >128241036-128241347                            11
## >25168373-25168611                              13
## >2:25168373-25168611                            12
## >25161598-25161833                              12
## >24283548-24283843                              10
## >7:24283548-24283843                             7
## >78358469-78358619                              11
## >7:128241036-1282413                            11
## >7:24283796-24283936                            14
## >6:31575210-31575467                            10
## >24283796-24283936                              10
## >2:25161598-25161833                            10
## >31575210-31575467                               9
## >17:78358469-7835861                            11
##                      >4:8288864-8288967 1632_103BP
## >128241036-128241347                            15
## >25168373-25168611                              14
## >2:25168373-25168611                            15
## >25161598-25161833                              13
## >24283548-24283843                              12
## >7:24283548-24283843                            11
## >78358469-78358619                               7
## >7:128241036-1282413                             5
## >7:24283796-24283936                            13
## >6:31575210-31575467                            11
## >24283796-24283936                               8
## >2:25161598-25161833                            12
## >31575210-31575467                              11
## >17:78358469-7835861                            12
##                      >8:22055623-22055743 2318_120BP
## >128241036-128241347                              14
## >25168373-25168611                                15
## >2:25168373-25168611                              15
## >25161598-25161833                                12
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >24283796-24283936                                10
## >2:25161598-25161833                              11
## >31575210-31575467                                11
## >17:78358469-7835861                              12
##                      >8288864-8288967 1632_103BP >5:10649438-10649513 4777_75BP
## >128241036-128241347                           9                             14
## >25168373-25168611                             8                             16
## >2:25168373-25168611                          10                              9
## >25161598-25161833                            14                             15
## >24283548-24283843                            10                             10
## >7:24283548-24283843                          12                             11
## >78358469-78358619                            14                             13
## >7:128241036-1282413                          16                             13
## >7:24283796-24283936                          13                             11
## >6:31575210-31575467                          13                             13
## >24283796-24283936                            12                             13
## >2:25161598-25161833                          17                             12
## >31575210-31575467                            13                             14
## >17:78358469-7835861                          16                             13
##                      >14989629-14989930 224_301BP
## >128241036-128241347                           11
## >25168373-25168611                             15
## >2:25168373-25168611                            8
## >25161598-25161833                             10
## >24283548-24283843                             12
## >7:24283548-24283843                           12
## >78358469-78358619                             15
## >7:128241036-1282413                           17
## >7:24283796-24283936                           11
## >6:31575210-31575467                           15
## >24283796-24283936                             15
## >2:25161598-25161833                           14
## >31575210-31575467                             15
## >17:78358469-7835861                           16
##                      >5:131945721-131945786 143_65BP
## >128241036-128241347                              11
## >25168373-25168611                                10
## >2:25168373-25168611                               8
## >25161598-25161833                                10
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >78358469-78358619                                16
## >7:128241036-1282413                              16
## >7:24283796-24283936                              13
## >6:31575210-31575467                              14
## >24283796-24283936                                13
## >2:25161598-25161833                              13
## >31575210-31575467                                16
## >17:78358469-7835861                              14
##                      >10649438-10649513 4777_75BP >22055623-22055743 2318_120BP
## >128241036-128241347                           12                             6
## >25168373-25168611                             14                             9
## >2:25168373-25168611                            8                            10
## >25161598-25161833                             10                             9
## >24283548-24283843                             10                            11
## >7:24283548-24283843                           12                            13
## >78358469-78358619                             16                            10
## >7:128241036-1282413                           15                            13
## >7:24283796-24283936                           14                            10
## >6:31575210-31575467                           15                             8
## >24283796-24283936                             14                            12
## >2:25161598-25161833                           11                            11
## >31575210-31575467                             13                            11
## >17:78358469-7835861                           12                            13
##                      >21:39108618-39108702 123_84BP >5:865245-865502 1593_257BP
## >128241036-128241347                             12                          11
## >25168373-25168611                               11                          13
## >2:25168373-25168611                             11                          10
## >25161598-25161833                               11                          11
## >24283548-24283843                               10                          12
## >7:24283548-24283843                             11                          13
## >78358469-78358619                               13                          14
## >7:128241036-1282413                             13                          14
## >7:24283796-24283936                             13                          14
## >6:31575210-31575467                             14                          13
## >24283796-24283936                               11                          12
## >2:25161598-25161833                             10                          11
## >31575210-31575467                               11                          12
## >17:78358469-7835861                             10                          10
##                      >16:14989629-14989930 224_301BP
## >128241036-128241347                               7
## >25168373-25168611                                 9
## >2:25168373-25168611                              12
## >25161598-25161833                                10
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >78358469-78358619                                14
## >7:128241036-1282413                              14
## >7:24283796-24283936                              13
## >6:31575210-31575467                              12
## >24283796-24283936                                14
## >2:25161598-25161833                              12
## >31575210-31575467                                13
## >17:78358469-7835861                              14
##                      >39108618-39108702 123_84BP >865245-865502 1593_257BP
## >128241036-128241347                           9                         9
## >25168373-25168611                            10                        10
## >2:25168373-25168611                          11                        12
## >25161598-25161833                             9                        11
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >78358469-78358619                            14                        15
## >7:128241036-1282413                          15                        15
## >7:24283796-24283936                          12                        12
## >6:31575210-31575467                          14                        13
## >24283796-24283936                            11                        13
## >2:25161598-25161833                          12                        10
## >31575210-31575467                            14                        14
## >17:78358469-7835861                          14                        14
## 
## [[13]]$rowDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 19.72308 
## 
## [[13]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 21.65641 
## 
## [[13]]$breaks
##  [1]  5.00  5.24  5.48  5.72  5.96  6.20  6.44  6.68  6.92  7.16  7.40  7.64
## [13]  7.88  8.12  8.36  8.60  8.84  9.08  9.32  9.56  9.80 10.04 10.28 10.52
## [25] 10.76 11.00 11.24 11.48 11.72 11.96 12.20 12.44 12.68 12.92 13.16 13.40
## [37] 13.64 13.88 14.12 14.36 14.60 14.84 15.08 15.32 15.56 15.80 16.04 16.28
## [49] 16.52 16.76 17.00
## 
## [[13]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[13]]$colorTable
##      low  high   color
## 1   5.00  5.24 #FF0000
## 2   5.24  5.48 #FF0505
## 3   5.48  5.72 #FF0A0A
## 4   5.72  5.96 #FF0F0F
## 5   5.96  6.20 #FF1414
## 6   6.20  6.44 #FF1A1A
## 7   6.44  6.68 #FF1F1F
## 8   6.68  6.92 #FF2424
## 9   6.92  7.16 #FF2929
## 10  7.16  7.40 #FF2E2E
## 11  7.40  7.64 #FF3434
## 12  7.64  7.88 #FF3939
## 13  7.88  8.12 #FF3E3E
## 14  8.12  8.36 #FF4343
## 15  8.36  8.60 #FF4848
## 16  8.60  8.84 #FF4E4E
## 17  8.84  9.08 #FF5353
## 18  9.08  9.32 #FF5858
## 19  9.32  9.56 #FF5D5D
## 20  9.56  9.80 #FF6262
## 21  9.80 10.04 #FF6868
## 22 10.04 10.28 #FF6D6D
## 23 10.28 10.52 #FF7272
## 24 10.52 10.76 #FF7777
## 25 10.76 11.00 #FF7C7C
## 26 11.00 11.24 #FF8282
## 27 11.24 11.48 #FF8787
## 28 11.48 11.72 #FF8C8C
## 29 11.72 11.96 #FF9191
## 30 11.96 12.20 #FF9696
## 31 12.20 12.44 #FF9C9C
## 32 12.44 12.68 #FFA1A1
## 33 12.68 12.92 #FFA6A6
## 34 12.92 13.16 #FFABAB
## 35 13.16 13.40 #FFB0B0
## 36 13.40 13.64 #FFB6B6
## 37 13.64 13.88 #FFBBBB
## 38 13.88 14.12 #FFC0C0
## 39 14.12 14.36 #FFC5C5
## 40 14.36 14.60 #FFCACA
## 41 14.60 14.84 #FFD0D0
## 42 14.84 15.08 #FFD5D5
## 43 15.08 15.32 #FFDADA
## 44 15.32 15.56 #FFDFDF
## 45 15.56 15.80 #FFE4E4
## 46 15.80 16.04 #FFEAEA
## 47 16.04 16.28 #FFEFEF
## 48 16.28 16.52 #FFF4F4
## 49 16.52 16.76 #FFF9F9
## 50 16.76 17.00 #FFFFFF
## 
## [[13]]$layout
## [[13]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[13]]$layout$lhei
## [1] 1.5 4.0
## 
## [[13]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[14]]
## [[14]]$rowInd
##  [1]  5 10 18  2 12 20 16 19  3  9  1 23 14 21  7 15 11  6 22 17 13  8  4 24
## 
## [[14]]$colInd
##  [1]  3  8 12  7 14  2  1 10 13  6  4  5  9 11
## 
## [[14]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[14]]$carpet
##                      >4:8288864-8288951 3145_87BP
## >2:25168373-25168611                           15
## >128241036-128241347                           15
## >25168373-25168611                             14
## >7:128241036-1282413                            5
## >78358469-78358619                              7
## >2:25161598-25161833                           12
## >17:78358469-7835861                           12
## >24283796-24283936                              8
## >31575210-31575467                             11
## >7:24283796-24283936                           13
## >6:31575210-31575467                           11
## >7:24283548-24283843                           11
## >24283548-24283843                             12
## >25161598-25161833                             13
##                      >8:22055623-22055743 4281_120BP
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25168373-25168611                                15
## >7:128241036-1282413                               7
## >78358469-78358619                                 7
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
## >24283796-24283936                                10
## >31575210-31575467                                11
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >7:24283548-24283843                              11
## >24283548-24283843                                12
## >25161598-25161833                                12
##                      >18611255-18611324 356_69BP >10:6307518-6307583 400_65BP
## >2:25168373-25168611                          17                           17
## >128241036-128241347                          17                           17
## >25168373-25168611                            16                           16
## >7:128241036-1282413                           7                            7
## >78358469-78358619                             8                            8
## >2:25161598-25161833                          10                           10
## >17:78358469-7835861                          10                           10
## >24283796-24283936                            12                           12
## >31575210-31575467                            10                           10
## >7:24283796-24283936                          12                           12
## >6:31575210-31575467                          13                           13
## >7:24283548-24283843                          14                           14
## >24283548-24283843                            14                           14
## >25161598-25161833                            14                           14
##                      >Y:12869910-12869975 354_65BP >43974366-43974508 202_142BP
## >2:25168373-25168611                            17                           11
## >128241036-128241347                            17                           10
## >25168373-25168611                              16                           12
## >7:128241036-1282413                             7                           10
## >78358469-78358619                               8                            8
## >2:25161598-25161833                            10                           11
## >17:78358469-7835861                            10                           11
## >24283796-24283936                              12                           10
## >31575210-31575467                              10                           11
## >7:24283796-24283936                            12                            7
## >6:31575210-31575467                            13                            8
## >7:24283548-24283843                            14                           12
## >24283548-24283843                              14                           11
## >25161598-25161833                              14                           11
##                      >14989690-14989869 171_179BP >22055623-22055743 4281_120BP
## >2:25168373-25168611                           12                            10
## >128241036-128241347                           12                             6
## >25168373-25168611                             13                             9
## >7:128241036-1282413                           10                            13
## >78358469-78358619                              8                            10
## >2:25161598-25161833                           11                            11
## >17:78358469-7835861                           12                            13
## >24283796-24283936                             12                            12
## >31575210-31575467                             13                            11
## >7:24283796-24283936                           11                            10
## >6:31575210-31575467                           10                             8
## >7:24283548-24283843                           12                            13
## >24283548-24283843                             10                            11
## >25161598-25161833                             11                             9
##                      >16:14989690-14989869 171_179BP
## >2:25168373-25168611                              12
## >128241036-128241347                               9
## >25168373-25168611                                10
## >7:128241036-1282413                              11
## >78358469-78358619                                13
## >2:25161598-25161833                               9
## >17:78358469-7835861                              14
## >24283796-24283936                                12
## >31575210-31575467                                10
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >7:24283548-24283843                              10
## >24283548-24283843                                12
## >25161598-25161833                                 9
##                      >7:63398191-63398273 101_82BP
## >2:25168373-25168611                            12
## >128241036-128241347                             9
## >25168373-25168611                               9
## >7:128241036-1282413                            11
## >78358469-78358619                              12
## >2:25161598-25161833                            10
## >17:78358469-7835861                            12
## >24283796-24283936                              14
## >31575210-31575467                              12
## >7:24283796-24283936                            10
## >6:31575210-31575467                            12
## >7:24283548-24283843                            13
## >24283548-24283843                              11
## >25161598-25161833                              10
##                      >1:18611255-18611324 356_69BP >8288864-8288951 3145_87BP
## >2:25168373-25168611                            10                         11
## >128241036-128241347                             4                          6
## >25168373-25168611                               8                         11
## >7:128241036-1282413                            15                         16
## >78358469-78358619                              16                         15
## >2:25161598-25161833                            15                         13
## >17:78358469-7835861                            14                         13
## >24283796-24283936                              13                         14
## >31575210-31575467                              12                         14
## >7:24283796-24283936                            12                         11
## >6:31575210-31575467                            12                         12
## >7:24283548-24283843                             9                          9
## >24283548-24283843                              11                         11
## >25161598-25161833                              11                         12
##                      >12869910-12869975 354_65BP >6307518-6307583 400_65BP
## >2:25168373-25168611                          10                        10
## >128241036-128241347                           7                         7
## >25168373-25168611                            11                        11
## >7:128241036-1282413                          16                        16
## >78358469-78358619                            14                        14
## >2:25161598-25161833                          15                        15
## >17:78358469-7835861                          11                        11
## >24283796-24283936                            13                        13
## >31575210-31575467                            13                        13
## >7:24283796-24283936                          12                        12
## >6:31575210-31575467                          10                        10
## >7:24283548-24283843                          12                        12
## >24283548-24283843                            10                        10
## >25161598-25161833                            12                        12
##                      >5:10649438-10649513 10108_75BP
## >2:25168373-25168611                               9
## >128241036-128241347                              14
## >25168373-25168611                                16
## >7:128241036-1282413                              13
## >78358469-78358619                                13
## >2:25161598-25161833                              12
## >17:78358469-7835861                              13
## >24283796-24283936                                13
## >31575210-31575467                                14
## >7:24283796-24283936                              11
## >6:31575210-31575467                              13
## >7:24283548-24283843                              11
## >24283548-24283843                                10
## >25161598-25161833                                15
##                      >131945721-131945800 4480_79BP
## >2:25168373-25168611                             11
## >128241036-128241347                             10
## >25168373-25168611                               12
## >7:128241036-1282413                             12
## >78358469-78358619                               14
## >2:25161598-25161833                             12
## >17:78358469-7835861                             10
## >24283796-24283936                               10
## >31575210-31575467                               12
## >7:24283796-24283936                             11
## >6:31575210-31575467                             11
## >7:24283548-24283843                             11
## >24283548-24283843                               12
## >25161598-25161833                               11
##                      >X:153420849-153420964 102_115BP
## >2:25168373-25168611                               12
## >128241036-128241347                               13
## >25168373-25168611                                 14
## >7:128241036-1282413                               12
## >78358469-78358619                                 13
## >2:25161598-25161833                               11
## >17:78358469-7835861                               10
## >24283796-24283936                                 10
## >31575210-31575467                                 11
## >7:24283796-24283936                               11
## >6:31575210-31575467                               12
## >7:24283548-24283843                               10
## >24283548-24283843                                 11
## >25161598-25161833                                 11
##                      >5:865245-865502 2678_257BP >63398191-63398273 101_82BP
## >2:25168373-25168611                          10                          11
## >128241036-128241347                          11                          12
## >25168373-25168611                            13                          13
## >7:128241036-1282413                          14                          14
## >78358469-78358619                            14                          14
## >2:25161598-25161833                          11                          12
## >17:78358469-7835861                          10                          11
## >24283796-24283936                            12                          13
## >31575210-31575467                            12                          14
## >7:24283796-24283936                          14                          11
## >6:31575210-31575467                          13                          12
## >7:24283548-24283843                          13                          13
## >24283548-24283843                            12                          11
## >25161598-25161833                            11                          11
##                      >153420849-153420964 102_115BP
## >2:25168373-25168611                              8
## >128241036-128241347                             11
## >25168373-25168611                               12
## >7:128241036-1282413                             14
## >78358469-78358619                               16
## >2:25161598-25161833                             11
## >17:78358469-7835861                             14
## >24283796-24283936                               13
## >31575210-31575467                               12
## >7:24283796-24283936                             16
## >6:31575210-31575467                             14
## >7:24283548-24283843                             10
## >24283548-24283843                               11
## >25161598-25161833                               10
##                      >10649438-10649513 10108_75BP
## >2:25168373-25168611                             8
## >128241036-128241347                            12
## >25168373-25168611                              14
## >7:128241036-1282413                            15
## >78358469-78358619                              16
## >2:25161598-25161833                            11
## >17:78358469-7835861                            12
## >24283796-24283936                              14
## >31575210-31575467                              13
## >7:24283796-24283936                            14
## >6:31575210-31575467                            15
## >7:24283548-24283843                            12
## >24283548-24283843                              10
## >25161598-25161833                              10
##                      >5:131945721-131945800 4480_79BP
## >2:25168373-25168611                                8
## >128241036-128241347                               11
## >25168373-25168611                                 10
## >7:128241036-1282413                               16
## >78358469-78358619                                 16
## >2:25161598-25161833                               13
## >17:78358469-7835861                               14
## >24283796-24283936                                 13
## >31575210-31575467                                 16
## >7:24283796-24283936                               13
## >6:31575210-31575467                               14
## >7:24283548-24283843                               12
## >24283548-24283843                                 10
## >25161598-25161833                                 10
##                      >22:43974366-43974508 202_142BP >865245-865502 2678_257BP
## >2:25168373-25168611                              11                        12
## >128241036-128241347                              10                         9
## >25168373-25168611                                 9                        10
## >7:128241036-1282413                              15                        15
## >78358469-78358619                                14                        15
## >2:25161598-25161833                              13                        10
## >17:78358469-7835861                              13                        14
## >24283796-24283936                                13                        13
## >31575210-31575467                                13                        14
## >7:24283796-24283936                              14                        12
## >6:31575210-31575467                              12                        13
## >7:24283548-24283843                              10                        12
## >24283548-24283843                                 9                        10
## >25161598-25161833                                10                        11
## 
## [[14]]$rowDendrogram
## 'dendrogram' with 2 branches and 24 members total, at height 22.36068 
## 
## [[14]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 31.87475 
## 
## [[14]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[14]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[14]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[14]]$layout
## [[14]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[14]]$layout$lhei
## [1] 1.5 4.0
## 
## [[14]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[15]]
## [[15]]$rowInd
##  [1]  8 13 11  4 10  6  5  9 16  7 14 12  1  3  2 15
## 
## [[15]]$colInd
##  [1]  7 14  2 10  1 13  3  8 12  6  4 11  9  5
## 
## [[15]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[15]]$carpet
##                      >8:22055623-22055743 4642_120BP
## >7:128241036-1282413                               7
## >78358469-78358619                                 7
## >2:25161598-25161833                              11
## >24283796-24283936                                10
## >17:78358469-7835861                              12
## >31575210-31575467                                11
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25168373-25168611                                15
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >25161598-25161833                                12
## >24283548-24283843                                12
## >7:24283548-24283843                              11
##                      >18611255-18611340 317_85BP >112387982-112388053 292_71BP
## >7:128241036-1282413                           7                             7
## >78358469-78358619                             8                             8
## >2:25161598-25161833                          10                            10
## >24283796-24283936                            12                            12
## >17:78358469-7835861                          10                            10
## >31575210-31575467                            10                            10
## >2:25168373-25168611                          17                            17
## >128241036-128241347                          17                            17
## >25168373-25168611                            16                            16
## >7:24283796-24283936                          12                            12
## >6:31575210-31575467                          13                            13
## >25161598-25161833                            14                            14
## >24283548-24283843                            14                            14
## >7:24283548-24283843                          14                            14
##                      >10:6307518-6307583 179_65BP >112387835-112387898 292_63BP
## >7:128241036-1282413                            7                             7
## >78358469-78358619                              8                             8
## >2:25161598-25161833                           10                            10
## >24283796-24283936                             12                            12
## >17:78358469-7835861                           10                            10
## >31575210-31575467                             10                            10
## >2:25168373-25168611                           17                            17
## >128241036-128241347                           17                            17
## >25168373-25168611                             16                            16
## >7:24283796-24283936                           12                            12
## >6:31575210-31575467                           13                            13
## >25161598-25161833                             14                            14
## >24283548-24283843                             14                            14
## >7:24283548-24283843                           14                            14
##                      >5:10649438-10649513 13348_75BP
## >7:128241036-1282413                              13
## >78358469-78358619                                13
## >2:25161598-25161833                              12
## >24283796-24283936                                13
## >17:78358469-7835861                              13
## >31575210-31575467                                14
## >2:25168373-25168611                               9
## >128241036-128241347                              14
## >25168373-25168611                                16
## >7:24283796-24283936                              11
## >6:31575210-31575467                              13
## >25161598-25161833                                15
## >24283548-24283843                                10
## >7:24283548-24283843                              11
##                      >5:865245-865502 1692_257BP >10649438-10649513 13348_75BP
## >7:128241036-1282413                          14                            15
## >78358469-78358619                            14                            16
## >2:25161598-25161833                          11                            11
## >24283796-24283936                            12                            14
## >17:78358469-7835861                          10                            12
## >31575210-31575467                            12                            13
## >2:25168373-25168611                          10                             8
## >128241036-128241347                          11                            12
## >25168373-25168611                            13                            14
## >7:24283796-24283936                          14                            14
## >6:31575210-31575467                          13                            15
## >25161598-25161833                            11                            10
## >24283548-24283843                            12                            10
## >7:24283548-24283843                          13                            12
##                      >865245-865502 1692_257BP >5:131945721-131945799 1965_78BP
## >7:128241036-1282413                        15                               16
## >78358469-78358619                          15                               16
## >2:25161598-25161833                        10                               13
## >24283796-24283936                          13                               13
## >17:78358469-7835861                        14                               14
## >31575210-31575467                          14                               16
## >2:25168373-25168611                        12                                8
## >128241036-128241347                         9                               11
## >25168373-25168611                          10                               10
## >7:24283796-24283936                        12                               13
## >6:31575210-31575467                        13                               14
## >25161598-25161833                          11                               10
## >24283548-24283843                          10                               10
## >7:24283548-24283843                        12                               12
##                      >22055623-22055743 4642_120BP
## >7:128241036-1282413                            13
## >78358469-78358619                              10
## >2:25161598-25161833                            11
## >24283796-24283936                              12
## >17:78358469-7835861                            13
## >31575210-31575467                              11
## >2:25168373-25168611                            10
## >128241036-128241347                             6
## >25168373-25168611                               9
## >7:24283796-24283936                            10
## >6:31575210-31575467                             8
## >25161598-25161833                               9
## >24283548-24283843                              11
## >7:24283548-24283843                            13
##                      >131945721-131945799 1965_78BP
## >7:128241036-1282413                             12
## >78358469-78358619                               12
## >2:25161598-25161833                             12
## >24283796-24283936                               10
## >17:78358469-7835861                             11
## >31575210-31575467                               11
## >2:25168373-25168611                             11
## >128241036-128241347                             11
## >25168373-25168611                               11
## >7:24283796-24283936                             10
## >6:31575210-31575467                             12
## >25161598-25161833                               10
## >24283548-24283843                               12
## >7:24283548-24283843                             10
##                      >1:18611255-18611340 317_85BP
## >7:128241036-1282413                            15
## >78358469-78358619                              16
## >2:25161598-25161833                            15
## >24283796-24283936                              13
## >17:78358469-7835861                            14
## >31575210-31575467                              12
## >2:25168373-25168611                            10
## >128241036-128241347                             4
## >25168373-25168611                               8
## >7:24283796-24283936                            12
## >6:31575210-31575467                            12
## >25161598-25161833                              11
## >24283548-24283843                              11
## >7:24283548-24283843                             9
##                      >1:112387982-112388053 292_71BP
## >7:128241036-1282413                              16
## >78358469-78358619                                16
## >2:25161598-25161833                              14
## >24283796-24283936                                15
## >17:78358469-7835861                              13
## >31575210-31575467                                13
## >2:25168373-25168611                              10
## >128241036-128241347                               7
## >25168373-25168611                                10
## >7:24283796-24283936                              11
## >6:31575210-31575467                              12
## >25161598-25161833                                11
## >24283548-24283843                                11
## >7:24283548-24283843                              11
##                      >1:112387835-112387898 292_63BP >6307518-6307583 179_65BP
## >7:128241036-1282413                              15                        16
## >78358469-78358619                                15                        14
## >2:25161598-25161833                              15                        15
## >24283796-24283936                                12                        13
## >17:78358469-7835861                              12                        11
## >31575210-31575467                                13                        13
## >2:25168373-25168611                              10                        10
## >128241036-128241347                               5                         7
## >25168373-25168611                                10                        11
## >7:24283796-24283936                              12                        12
## >6:31575210-31575467                              11                        10
## >25161598-25161833                                12                        12
## >24283548-24283843                                10                        10
## >7:24283548-24283843                              11                        12
## 
## [[15]]$rowDendrogram
## 'dendrogram' with 2 branches and 16 members total, at height 22.36068 
## 
## [[15]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 31.01612 
## 
## [[15]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[15]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[15]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[15]]$layout
## [[15]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[15]]$layout$lhei
## [1] 1.5 4.0
## 
## [[15]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[16]]
## [[16]]$rowInd
##  [1] 15 17 22  5  9 19  2 12 20  3  1 23 14 21 10 11  7  8 24  4  6 13 16 18
## 
## [[16]]$colInd
##  [1] 14  7  3  8 12 11  2  9  5  4  6 10 13  1
## 
## [[16]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[16]]$carpet
##                      >131945721-131945786 1012_65BP
## >78358469-78358619                               11
## >7:128241036-1282413                             11
## >2:25168373-25168611                             12
## >128241036-128241347                             11
## >25168373-25168611                               13
## >25161598-25161833                               12
## >2:25161598-25161833                             10
## >24283548-24283843                               10
## >7:24283548-24283843                              7
## >6:31575210-31575467                             10
## >7:24283796-24283936                             14
## >24283796-24283936                               10
## >31575210-31575467                                9
## >17:78358469-7835861                             11
##                      >14989694-14989865 108_171BP >80568673-80568788 280_115BP
## >78358469-78358619                             10                           11
## >7:128241036-1282413                           14                           10
## >2:25168373-25168611                           11                           15
## >128241036-128241347                           14                           14
## >25168373-25168611                             14                           13
## >25161598-25161833                             10                           11
## >2:25161598-25161833                           10                           12
## >24283548-24283843                             11                           12
## >7:24283548-24283843                           12                           12
## >6:31575210-31575467                           14                           15
## >7:24283796-24283936                            9                           11
## >24283796-24283936                             13                           10
## >31575210-31575467                             11                            9
## >17:78358469-7835861                           13                           11
##                      >4:8288864-8288929 125_65BP
## >78358469-78358619                             7
## >7:128241036-1282413                           5
## >2:25168373-25168611                          15
## >128241036-128241347                          15
## >25168373-25168611                            14
## >25161598-25161833                            13
## >2:25161598-25161833                          12
## >24283548-24283843                            12
## >7:24283548-24283843                          11
## >6:31575210-31575467                          11
## >7:24283796-24283936                          13
## >24283796-24283936                             8
## >31575210-31575467                            11
## >17:78358469-7835861                          12
##                      >8:22055623-22055743 1943_120BP
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25168373-25168611                                15
## >25161598-25161833                                12
## >2:25161598-25161833                              11
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >24283796-24283936                                10
## >31575210-31575467                                11
## >17:78358469-7835861                              12
##                      >18611255-18611344 564_89BP >10:6307512-6307583 246_71BP
## >78358469-78358619                             8                            8
## >7:128241036-1282413                           7                            7
## >2:25168373-25168611                          17                           17
## >128241036-128241347                          17                           17
## >25168373-25168611                            16                           16
## >25161598-25161833                            14                           14
## >2:25161598-25161833                          10                           10
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >6:31575210-31575467                          13                           13
## >7:24283796-24283936                          12                           12
## >24283796-24283936                            12                           12
## >31575210-31575467                            10                           10
## >17:78358469-7835861                          10                           10
##                      >Y:12869910-12869975 183_65BP
## >78358469-78358619                               8
## >7:128241036-1282413                             7
## >2:25168373-25168611                            17
## >128241036-128241347                            17
## >25168373-25168611                              16
## >25161598-25161833                              14
## >2:25161598-25161833                            10
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >6:31575210-31575467                            13
## >7:24283796-24283936                            12
## >24283796-24283936                              12
## >31575210-31575467                              10
## >17:78358469-7835861                            10
##                      >22055623-22055743 1943_120BP
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >2:25168373-25168611                            10
## >128241036-128241347                             6
## >25168373-25168611                               9
## >25161598-25161833                               9
## >2:25161598-25161833                            11
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >6:31575210-31575467                             8
## >7:24283796-24283936                            10
## >24283796-24283936                              12
## >31575210-31575467                              11
## >17:78358469-7835861                            13
##                      >11:80568673-80568788 280_115BP
## >78358469-78358619                                10
## >7:128241036-1282413                              12
## >2:25168373-25168611                              13
## >128241036-128241347                               9
## >25168373-25168611                                11
## >25161598-25161833                                 9
## >2:25161598-25161833                              11
## >24283548-24283843                                13
## >7:24283548-24283843                              15
## >6:31575210-31575467                               8
## >7:24283796-24283936                               9
## >24283796-24283936                                11
## >31575210-31575467                                 9
## >17:78358469-7835861                              12
##                      >1:18611255-18611344 564_89BP >8288864-8288929 125_65BP
## >78358469-78358619                              16                        15
## >7:128241036-1282413                            15                        15
## >2:25168373-25168611                            10                        10
## >128241036-128241347                             4                         9
## >25168373-25168611                               8                         9
## >25161598-25161833                              11                        12
## >2:25161598-25161833                            15                        16
## >24283548-24283843                              11                        10
## >7:24283548-24283843                             9                        10
## >6:31575210-31575467                            12                        13
## >7:24283796-24283936                            12                        11
## >24283796-24283936                              13                        12
## >31575210-31575467                              12                        14
## >17:78358469-7835861                            14                        14
##                      >12869910-12869975 183_65BP >6307512-6307583 246_71BP
## >78358469-78358619                            14                        14
## >7:128241036-1282413                          16                        16
## >2:25168373-25168611                          10                        10
## >128241036-128241347                           7                         7
## >25168373-25168611                            11                        11
## >25161598-25161833                            12                        12
## >2:25161598-25161833                          15                        15
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >6:31575210-31575467                          10                        10
## >7:24283796-24283936                          12                        12
## >24283796-24283936                            13                        13
## >31575210-31575467                            13                        13
## >17:78358469-7835861                          11                        11
##                      >KI270733.1:133694-133777 106_83BP
## >78358469-78358619                                   18
## >7:128241036-1282413                                 19
## >2:25168373-25168611                                 12
## >128241036-128241347                                 13
## >25168373-25168611                                   14
## >25161598-25161833                                   11
## >2:25161598-25161833                                 10
## >24283548-24283843                                   15
## >7:24283548-24283843                                 13
## >6:31575210-31575467                                 16
## >7:24283796-24283936                                 14
## >24283796-24283936                                   18
## >31575210-31575467                                   16
## >17:78358469-7835861                                 15
##                      >KI270733.1:178774-178856 105_82BP
## >78358469-78358619                                   17
## >7:128241036-1282413                                 19
## >2:25168373-25168611                                 12
## >128241036-128241347                                 13
## >25168373-25168611                                   15
## >25161598-25161833                                   10
## >2:25161598-25161833                                 12
## >24283548-24283843                                   15
## >7:24283548-24283843                                 14
## >6:31575210-31575467                                 16
## >7:24283796-24283936                                 14
## >24283796-24283936                                   16
## >31575210-31575467                                   17
## >17:78358469-7835861                                 15
##                      >5:10649438-10649513 8843_75BP
## >78358469-78358619                               13
## >7:128241036-1282413                             13
## >2:25168373-25168611                              9
## >128241036-128241347                             14
## >25168373-25168611                               16
## >25161598-25161833                               15
## >2:25161598-25161833                             12
## >24283548-24283843                               10
## >7:24283548-24283843                             11
## >6:31575210-31575467                             13
## >7:24283796-24283936                             11
## >24283796-24283936                               13
## >31575210-31575467                               14
## >17:78358469-7835861                             13
##                      >5:131945721-131945786 1012_65BP >865245-865502 1566_257BP
## >78358469-78358619                                 16                        15
## >7:128241036-1282413                               16                        15
## >2:25168373-25168611                                8                        12
## >128241036-128241347                               11                         9
## >25168373-25168611                                 10                        10
## >25161598-25161833                                 10                        11
## >2:25161598-25161833                               13                        10
## >24283548-24283843                                 10                        10
## >7:24283548-24283843                               12                        12
## >6:31575210-31575467                               14                        13
## >7:24283796-24283936                               13                        12
## >24283796-24283936                                 13                        13
## >31575210-31575467                                 16                        14
## >17:78358469-7835861                               14                        14
##                      >16:14989694-14989865 108_171BP
## >78358469-78358619                                14
## >7:128241036-1282413                              14
## >2:25168373-25168611                              13
## >128241036-128241347                              12
## >25168373-25168611                                10
## >25161598-25161833                                 9
## >2:25161598-25161833                              11
## >24283548-24283843                                12
## >7:24283548-24283843                              14
## >6:31575210-31575467                              14
## >7:24283796-24283936                              12
## >24283796-24283936                                13
## >31575210-31575467                                13
## >17:78358469-7835861                              14
##                      >5:865245-865502 1566_257BP >10649438-10649513 8843_75BP
## >78358469-78358619                            14                           16
## >7:128241036-1282413                          14                           15
## >2:25168373-25168611                          10                            8
## >128241036-128241347                          11                           12
## >25168373-25168611                            13                           14
## >25161598-25161833                            11                           10
## >2:25161598-25161833                          11                           11
## >24283548-24283843                            12                           10
## >7:24283548-24283843                          13                           12
## >6:31575210-31575467                          13                           15
## >7:24283796-24283936                          14                           14
## >24283796-24283936                            12                           14
## >31575210-31575467                            12                           13
## >17:78358469-7835861                          10                           12
##                      >133694-133777 106_83BP >178774-178856 105_82BP
## >78358469-78358619                        16                      16
## >7:128241036-1282413                      16                      16
## >2:25168373-25168611                      10                      10
## >128241036-128241347                      11                      11
## >25168373-25168611                        13                      13
## >25161598-25161833                        11                      11
## >2:25161598-25161833                      12                      12
## >24283548-24283843                        14                      14
## >7:24283548-24283843                      13                      13
## >6:31575210-31575467                      16                      16
## >7:24283796-24283936                      13                      13
## >24283796-24283936                        13                      13
## >31575210-31575467                        12                      12
## >17:78358469-7835861                      13                      13
## 
## [[16]]$rowDendrogram
## 'dendrogram' with 2 branches and 24 members total, at height 22.60531 
## 
## [[16]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 32.37283 
## 
## [[16]]$breaks
##  [1]  4.0  4.3  4.6  4.9  5.2  5.5  5.8  6.1  6.4  6.7  7.0  7.3  7.6  7.9  8.2
## [16]  8.5  8.8  9.1  9.4  9.7 10.0 10.3 10.6 10.9 11.2 11.5 11.8 12.1 12.4 12.7
## [31] 13.0 13.3 13.6 13.9 14.2 14.5 14.8 15.1 15.4 15.7 16.0 16.3 16.6 16.9 17.2
## [46] 17.5 17.8 18.1 18.4 18.7 19.0
## 
## [[16]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[16]]$colorTable
##     low high   color
## 1   4.0  4.3 #FF0000
## 2   4.3  4.6 #FF0505
## 3   4.6  4.9 #FF0A0A
## 4   4.9  5.2 #FF0F0F
## 5   5.2  5.5 #FF1414
## 6   5.5  5.8 #FF1A1A
## 7   5.8  6.1 #FF1F1F
## 8   6.1  6.4 #FF2424
## 9   6.4  6.7 #FF2929
## 10  6.7  7.0 #FF2E2E
## 11  7.0  7.3 #FF3434
## 12  7.3  7.6 #FF3939
## 13  7.6  7.9 #FF3E3E
## 14  7.9  8.2 #FF4343
## 15  8.2  8.5 #FF4848
## 16  8.5  8.8 #FF4E4E
## 17  8.8  9.1 #FF5353
## 18  9.1  9.4 #FF5858
## 19  9.4  9.7 #FF5D5D
## 20  9.7 10.0 #FF6262
## 21 10.0 10.3 #FF6868
## 22 10.3 10.6 #FF6D6D
## 23 10.6 10.9 #FF7272
## 24 10.9 11.2 #FF7777
## 25 11.2 11.5 #FF7C7C
## 26 11.5 11.8 #FF8282
## 27 11.8 12.1 #FF8787
## 28 12.1 12.4 #FF8C8C
## 29 12.4 12.7 #FF9191
## 30 12.7 13.0 #FF9696
## 31 13.0 13.3 #FF9C9C
## 32 13.3 13.6 #FFA1A1
## 33 13.6 13.9 #FFA6A6
## 34 13.9 14.2 #FFABAB
## 35 14.2 14.5 #FFB0B0
## 36 14.5 14.8 #FFB6B6
## 37 14.8 15.1 #FFBBBB
## 38 15.1 15.4 #FFC0C0
## 39 15.4 15.7 #FFC5C5
## 40 15.7 16.0 #FFCACA
## 41 16.0 16.3 #FFD0D0
## 42 16.3 16.6 #FFD5D5
## 43 16.6 16.9 #FFDADA
## 44 16.9 17.2 #FFDFDF
## 45 17.2 17.5 #FFE4E4
## 46 17.5 17.8 #FFEAEA
## 47 17.8 18.1 #FFEFEF
## 48 18.1 18.4 #FFF4F4
## 49 18.4 18.7 #FFF9F9
## 50 18.7 19.0 #FFFFFF
## 
## [[16]]$layout
## [[16]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[16]]$layout$lhei
## [1] 1.5 4.0
## 
## [[16]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[17]]
## [[17]]$rowInd
##  [1]  5  9  3 11 12  7 15  6 10 16  8 13  4 14  1 17  2 18
## 
## [[17]]$colInd
##  [1]  3  9  5 11  8 12  7 14  6 10  4  2 13  1
## 
## [[17]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[17]]$carpet
##                      >4:8288864-8288951 1128_87BP
## >2:25168373-25168611                           15
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >25161598-25161833                             13
## >128241036-128241347                           15
## >25168373-25168611                             14
## >7:128241036-1282413                            5
## >78358469-78358619                              7
## >7:24283796-24283936                           13
## >24283796-24283936                              8
## >6:31575210-31575467                           11
## >2:25161598-25161833                           12
## >31575210-31575467                             11
## >17:78358469-7835861                           12
##                      >8:22055623-22055726 870_103BP
## >2:25168373-25168611                             15
## >24283548-24283843                               12
## >7:24283548-24283843                             11
## >25161598-25161833                               12
## >128241036-128241347                             14
## >25168373-25168611                               15
## >7:128241036-1282413                              7
## >78358469-78358619                                7
## >7:24283796-24283936                             12
## >24283796-24283936                               10
## >6:31575210-31575467                             13
## >2:25161598-25161833                             11
## >31575210-31575467                               11
## >17:78358469-7835861                             12
##                      >17:4550782-4550844 390_62BP >11551551-11551692 224_141BP
## >2:25168373-25168611                           10                           10
## >24283548-24283843                             11                            9
## >7:24283548-24283843                           11                           10
## >25161598-25161833                             13                           12
## >128241036-128241347                           11                           12
## >25168373-25168611                             12                           13
## >7:128241036-1282413                           10                           10
## >78358469-78358619                             10                            9
## >7:24283796-24283936                           14                           13
## >24283796-24283936                             10                           11
## >6:31575210-31575467                           10                           11
## >2:25161598-25161833                           15                           10
## >31575210-31575467                             13                           10
## >17:78358469-7835861                           13                           10
##                      >131945721-131945786 1272_65BP
## >2:25168373-25168611                             12
## >24283548-24283843                               10
## >7:24283548-24283843                              7
## >25161598-25161833                               12
## >128241036-128241347                             11
## >25168373-25168611                               13
## >7:128241036-1282413                             11
## >78358469-78358619                               11
## >7:24283796-24283936                             14
## >24283796-24283936                               10
## >6:31575210-31575467                             10
## >2:25161598-25161833                             10
## >31575210-31575467                                9
## >17:78358469-7835861                             11
##                      >5:10649438-10649513 7273_75BP
## >2:25168373-25168611                              9
## >24283548-24283843                               10
## >7:24283548-24283843                             11
## >25161598-25161833                               15
## >128241036-128241347                             14
## >25168373-25168611                               16
## >7:128241036-1282413                             13
## >78358469-78358619                               13
## >7:24283796-24283936                             11
## >24283796-24283936                               13
## >6:31575210-31575467                             13
## >2:25161598-25161833                             12
## >31575210-31575467                               14
## >17:78358469-7835861                             13
##                      >43926216-43926323 356_107BP >5:865245-865502 2330_257BP
## >2:25168373-25168611                            6                          10
## >24283548-24283843                              9                          12
## >7:24283548-24283843                           12                          13
## >25161598-25161833                             14                          11
## >128241036-128241347                           12                          11
## >25168373-25168611                             14                          13
## >7:128241036-1282413                           14                          14
## >78358469-78358619                             15                          14
## >7:24283796-24283936                           13                          14
## >24283796-24283936                             13                          12
## >6:31575210-31575467                           14                          13
## >2:25161598-25161833                           12                          11
## >31575210-31575467                             10                          12
## >17:78358469-7835861                           10                          10
##                      >10649438-10649513 7273_75BP >4550782-4550844 390_62BP
## >2:25168373-25168611                            8                        11
## >24283548-24283843                             10                        12
## >7:24283548-24283843                           12                        10
## >25161598-25161833                             10                         9
## >128241036-128241347                           12                        12
## >25168373-25168611                             14                        11
## >7:128241036-1282413                           15                        17
## >78358469-78358619                             16                        15
## >7:24283796-24283936                           14                        14
## >24283796-24283936                             14                        14
## >6:31575210-31575467                           15                        17
## >2:25161598-25161833                           11                        15
## >31575210-31575467                             13                        14
## >17:78358469-7835861                           12                        17
##                      >5:131945721-131945786 1272_65BP
## >2:25168373-25168611                                8
## >24283548-24283843                                 10
## >7:24283548-24283843                               12
## >25161598-25161833                                 10
## >128241036-128241347                               11
## >25168373-25168611                                 10
## >7:128241036-1282413                               16
## >78358469-78358619                                 16
## >7:24283796-24283936                               13
## >24283796-24283936                                 13
## >6:31575210-31575467                               14
## >2:25161598-25161833                               13
## >31575210-31575467                                 16
## >17:78358469-7835861                               14
##                      >14989629-14989930 219_301BP
## >2:25168373-25168611                            8
## >24283548-24283843                             12
## >7:24283548-24283843                           12
## >25161598-25161833                             10
## >128241036-128241347                           11
## >25168373-25168611                             15
## >7:128241036-1282413                           17
## >78358469-78358619                             15
## >7:24283796-24283936                           11
## >24283796-24283936                             15
## >6:31575210-31575467                           15
## >2:25161598-25161833                           14
## >31575210-31575467                             15
## >17:78358469-7835861                           16
##                      >19:11551551-11551692 224_141BP
## >2:25168373-25168611                              11
## >24283548-24283843                                 7
## >7:24283548-24283843                              11
## >25161598-25161833                                10
## >128241036-128241347                               9
## >25168373-25168611                                 8
## >7:128241036-1282413                              14
## >78358469-78358619                                15
## >7:24283796-24283936                              13
## >24283796-24283936                                14
## >6:31575210-31575467                              14
## >2:25161598-25161833                              13
## >31575210-31575467                                14
## >17:78358469-7835861                              14
##                      >22055623-22055726 870_103BP
## >2:25168373-25168611                            9
## >24283548-24283843                              9
## >7:24283548-24283843                            9
## >25161598-25161833                             12
## >128241036-128241347                            9
## >25168373-25168611                              9
## >7:128241036-1282413                           14
## >78358469-78358619                             14
## >7:24283796-24283936                           12
## >24283796-24283936                             12
## >6:31575210-31575467                           13
## >2:25161598-25161833                           14
## >31575210-31575467                             12
## >17:78358469-7835861                           14
##                      >1:43926216-43926323 356_107BP >8288864-8288951 1128_87BP
## >2:25168373-25168611                             12                         11
## >24283548-24283843                                9                         11
## >7:24283548-24283843                             10                          9
## >25161598-25161833                               11                         12
## >128241036-128241347                              8                          6
## >25168373-25168611                                9                         11
## >7:128241036-1282413                             13                         16
## >78358469-78358619                               15                         15
## >7:24283796-24283936                             14                         11
## >24283796-24283936                               12                         14
## >6:31575210-31575467                             13                         12
## >2:25161598-25161833                             12                         13
## >31575210-31575467                               11                         14
## >17:78358469-7835861                             14                         13
##                      >16:14989629-14989930 219_301BP >865245-865502 2330_257BP
## >2:25168373-25168611                              12                        12
## >24283548-24283843                                10                        10
## >7:24283548-24283843                              12                        12
## >25161598-25161833                                10                        11
## >128241036-128241347                               7                         9
## >25168373-25168611                                 9                        10
## >7:128241036-1282413                              14                        15
## >78358469-78358619                                14                        15
## >7:24283796-24283936                              13                        12
## >24283796-24283936                                14                        13
## >6:31575210-31575467                              12                        13
## >2:25161598-25161833                              12                        10
## >31575210-31575467                                13                        14
## >17:78358469-7835861                              14                        14
## 
## [[17]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 19.72308 
## 
## [[17]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 23.74868 
## 
## [[17]]$breaks
##  [1]  5.00  5.24  5.48  5.72  5.96  6.20  6.44  6.68  6.92  7.16  7.40  7.64
## [13]  7.88  8.12  8.36  8.60  8.84  9.08  9.32  9.56  9.80 10.04 10.28 10.52
## [25] 10.76 11.00 11.24 11.48 11.72 11.96 12.20 12.44 12.68 12.92 13.16 13.40
## [37] 13.64 13.88 14.12 14.36 14.60 14.84 15.08 15.32 15.56 15.80 16.04 16.28
## [49] 16.52 16.76 17.00
## 
## [[17]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[17]]$colorTable
##      low  high   color
## 1   5.00  5.24 #FF0000
## 2   5.24  5.48 #FF0505
## 3   5.48  5.72 #FF0A0A
## 4   5.72  5.96 #FF0F0F
## 5   5.96  6.20 #FF1414
## 6   6.20  6.44 #FF1A1A
## 7   6.44  6.68 #FF1F1F
## 8   6.68  6.92 #FF2424
## 9   6.92  7.16 #FF2929
## 10  7.16  7.40 #FF2E2E
## 11  7.40  7.64 #FF3434
## 12  7.64  7.88 #FF3939
## 13  7.88  8.12 #FF3E3E
## 14  8.12  8.36 #FF4343
## 15  8.36  8.60 #FF4848
## 16  8.60  8.84 #FF4E4E
## 17  8.84  9.08 #FF5353
## 18  9.08  9.32 #FF5858
## 19  9.32  9.56 #FF5D5D
## 20  9.56  9.80 #FF6262
## 21  9.80 10.04 #FF6868
## 22 10.04 10.28 #FF6D6D
## 23 10.28 10.52 #FF7272
## 24 10.52 10.76 #FF7777
## 25 10.76 11.00 #FF7C7C
## 26 11.00 11.24 #FF8282
## 27 11.24 11.48 #FF8787
## 28 11.48 11.72 #FF8C8C
## 29 11.72 11.96 #FF9191
## 30 11.96 12.20 #FF9696
## 31 12.20 12.44 #FF9C9C
## 32 12.44 12.68 #FFA1A1
## 33 12.68 12.92 #FFA6A6
## 34 12.92 13.16 #FFABAB
## 35 13.16 13.40 #FFB0B0
## 36 13.40 13.64 #FFB6B6
## 37 13.64 13.88 #FFBBBB
## 38 13.88 14.12 #FFC0C0
## 39 14.12 14.36 #FFC5C5
## 40 14.36 14.60 #FFCACA
## 41 14.60 14.84 #FFD0D0
## 42 14.84 15.08 #FFD5D5
## 43 15.08 15.32 #FFDADA
## 44 15.32 15.56 #FFDFDF
## 45 15.56 15.80 #FFE4E4
## 46 15.80 16.04 #FFEAEA
## 47 16.04 16.28 #FFEFEF
## 48 16.28 16.52 #FFF4F4
## 49 16.52 16.76 #FFF9F9
## 50 16.76 17.00 #FFFFFF
## 
## [[17]]$layout
## [[17]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[17]]$layout$lhei
## [1] 1.5 4.0
## 
## [[17]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[18]]
## [[18]]$rowInd
##  [1]  7 10  1 12  9  2 11 13  3  5  4  8 14  6
## 
## [[18]]$colInd
##  [1]  8 12  5  3  9 11 14  7  2  1  4  6 10 13
## 
## [[18]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[18]]$carpet
##                      >8:22055623-22055743 2893_120BP
## >128241036-128241347                              14
## >25168373-25168611                                15
## >7:24283548-24283843                              11
## >2:25168373-25168611                              15
## >24283548-24283843                                12
## >25161598-25161833                                12
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >24283796-24283936                                10
## >31575210-31575467                                11
##                      >18611255-18611336 529_81BP >1:18611255-18611336 529_81BP
## >128241036-128241347                          17                             4
## >25168373-25168611                            16                             8
## >7:24283548-24283843                          14                             9
## >2:25168373-25168611                          17                            10
## >24283548-24283843                            14                            11
## >25161598-25161833                            14                            11
## >78358469-78358619                             8                            16
## >7:128241036-1282413                           7                            15
## >2:25161598-25161833                          10                            15
## >17:78358469-7835861                          10                            14
## >6:31575210-31575467                          13                            12
## >7:24283796-24283936                          12                            12
## >24283796-24283936                            12                            13
## >31575210-31575467                            10                            12
##                      >4550782-4550844 150_62BP >131945721-131945786 1525_65BP
## >128241036-128241347                        12                             11
## >25168373-25168611                          11                             13
## >7:24283548-24283843                        10                              7
## >2:25168373-25168611                        11                             12
## >24283548-24283843                          12                             10
## >25161598-25161833                           9                             12
## >78358469-78358619                          15                             11
## >7:128241036-1282413                        17                             11
## >2:25161598-25161833                        15                             10
## >17:78358469-7835861                        17                             11
## >6:31575210-31575467                        17                             10
## >7:24283796-24283936                        14                             14
## >24283796-24283936                          14                             10
## >31575210-31575467                          14                              9
##                      >17:4550782-4550844 150_62BP >22055623-22055743 2893_120BP
## >128241036-128241347                           11                             6
## >25168373-25168611                             12                             9
## >7:24283548-24283843                           11                            13
## >2:25168373-25168611                           10                            10
## >24283548-24283843                             11                            11
## >25161598-25161833                             13                             9
## >78358469-78358619                             10                            10
## >7:128241036-1282413                           10                            13
## >2:25161598-25161833                           15                            11
## >17:78358469-7835861                           13                            13
## >6:31575210-31575467                           10                             8
## >7:24283796-24283936                           14                            10
## >24283796-24283936                             10                            12
## >31575210-31575467                             13                            11
##                      >62060954-62061019 288_65BP >17:62060954-62061019 288_65BP
## >128241036-128241347                          12                             12
## >25168373-25168611                            10                             10
## >7:24283548-24283843                          15                             12
## >2:25168373-25168611                          13                             14
## >24283548-24283843                            10                             11
## >25161598-25161833                             9                             11
## >78358469-78358619                             7                             11
## >7:128241036-1282413                          12                             13
## >2:25161598-25161833                          13                             14
## >17:78358469-7835861                          12                             14
## >6:31575210-31575467                           9                             13
## >7:24283796-24283936                          11                             10
## >24283796-24283936                            10                             11
## >31575210-31575467                            12                             11
##                      >5:10649438-10649513 16465_75BP >5:865245-865502 834_257BP
## >128241036-128241347                              14                         11
## >25168373-25168611                                16                         13
## >7:24283548-24283843                              11                         13
## >2:25168373-25168611                               9                         10
## >24283548-24283843                                10                         12
## >25161598-25161833                                15                         11
## >78358469-78358619                                13                         14
## >7:128241036-1282413                              13                         14
## >2:25161598-25161833                              12                         11
## >17:78358469-7835861                              13                         10
## >6:31575210-31575467                              13                         13
## >7:24283796-24283936                              11                         14
## >24283796-24283936                                13                         12
## >31575210-31575467                                14                         12
##                      >10649438-10649513 16465_75BP >865245-865502 834_257BP
## >128241036-128241347                            12                        9
## >25168373-25168611                              14                       10
## >7:24283548-24283843                            12                       12
## >2:25168373-25168611                             8                       12
## >24283548-24283843                              10                       10
## >25161598-25161833                              10                       11
## >78358469-78358619                              16                       15
## >7:128241036-1282413                            15                       15
## >2:25161598-25161833                            11                       10
## >17:78358469-7835861                            12                       14
## >6:31575210-31575467                            15                       13
## >7:24283796-24283936                            14                       12
## >24283796-24283936                              14                       13
## >31575210-31575467                              13                       14
##                      >5:131945721-131945786 1525_65BP
## >128241036-128241347                               11
## >25168373-25168611                                 10
## >7:24283548-24283843                               12
## >2:25168373-25168611                                8
## >24283548-24283843                                 10
## >25161598-25161833                                 10
## >78358469-78358619                                 16
## >7:128241036-1282413                               16
## >2:25161598-25161833                               13
## >17:78358469-7835861                               14
## >6:31575210-31575467                               14
## >7:24283796-24283936                               13
## >24283796-24283936                                 13
## >31575210-31575467                                 16
## 
## [[18]]$rowDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 22.36068 
## 
## [[18]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 20.63977 
## 
## [[18]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[18]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[18]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[18]]$layout
## [[18]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[18]]$layout$lhei
## [1] 1.5 4.0
## 
## [[18]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[19]]
## [[19]]$rowInd
##  [1]  6 10  2 15 16 18  1 19 13  7  4 20  8 17  3 11 12 14  5  9
## 
## [[19]]$colInd
##  [1]  8 12  3 11  9  5 14  7  2  1 13 10  6  4
## 
## [[19]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[19]]$carpet
##                      >4:8288864-8288951 2350_87BP
## >128241036-128241347                           15
## >25168373-25168611                             14
## >2:25168373-25168611                           15
## >25161598-25161833                             13
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >78358469-78358619                              7
## >7:128241036-1282413                            5
## >2:25161598-25161833                           12
## >17:78358469-7835861                           12
## >31575210-31575467                             11
## >24283796-24283936                              8
## >7:24283796-24283936                           13
## >6:31575210-31575467                           11
##                      >8:22055623-22055743 3973_120BP
## >128241036-128241347                              14
## >25168373-25168611                                15
## >2:25168373-25168611                              15
## >25161598-25161833                                12
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25161598-25161833                              11
## >17:78358469-7835861                              12
## >31575210-31575467                                11
## >24283796-24283936                                10
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
##                      >10:6307508-6307583 230_75BP >18611255-18611336 315_81BP
## >128241036-128241347                           17                          17
## >25168373-25168611                             16                          16
## >2:25168373-25168611                           17                          17
## >25161598-25161833                             14                          14
## >24283548-24283843                             14                          14
## >7:24283548-24283843                           14                          14
## >78358469-78358619                              8                           8
## >7:128241036-1282413                            7                           7
## >2:25161598-25161833                           10                          10
## >17:78358469-7835861                           10                          10
## >31575210-31575467                             10                          10
## >24283796-24283936                             12                          12
## >7:24283796-24283936                           12                          12
## >6:31575210-31575467                           13                          13
##                      >22055623-22055743 3973_120BP >6307508-6307583 230_75BP
## >128241036-128241347                             6                         7
## >25168373-25168611                               9                        11
## >2:25168373-25168611                            10                        10
## >25161598-25161833                               9                        12
## >24283548-24283843                              11                        10
## >7:24283548-24283843                            13                        12
## >78358469-78358619                              10                        14
## >7:128241036-1282413                            13                        16
## >2:25161598-25161833                            11                        15
## >17:78358469-7835861                            13                        11
## >31575210-31575467                              11                        13
## >24283796-24283936                              12                        13
## >7:24283796-24283936                            10                        12
## >6:31575210-31575467                             8                        10
##                      >1:18611255-18611336 315_81BP >8288864-8288951 2350_87BP
## >128241036-128241347                             4                          6
## >25168373-25168611                               8                         11
## >2:25168373-25168611                            10                         11
## >25161598-25161833                              11                         12
## >24283548-24283843                              11                         11
## >7:24283548-24283843                             9                          9
## >78358469-78358619                              16                         15
## >7:128241036-1282413                            15                         16
## >2:25161598-25161833                            15                         13
## >17:78358469-7835861                            14                         13
## >31575210-31575467                              12                         14
## >24283796-24283936                              13                         14
## >7:24283796-24283936                            12                         11
## >6:31575210-31575467                            12                         12
##                      >131945721-131945800 2391_79BP >5:865245-865502 1249_257BP
## >128241036-128241347                             10                          11
## >25168373-25168611                               12                          13
## >2:25168373-25168611                             11                          10
## >25161598-25161833                               11                          11
## >24283548-24283843                               12                          12
## >7:24283548-24283843                             11                          13
## >78358469-78358619                               14                          14
## >7:128241036-1282413                             12                          14
## >2:25161598-25161833                             12                          11
## >17:78358469-7835861                             10                          10
## >31575210-31575467                               12                          12
## >24283796-24283936                               10                          12
## >7:24283796-24283936                             11                          14
## >6:31575210-31575467                             11                          13
##                      >16:14989629-14989930 213_301BP >865245-865502 1249_257BP
## >128241036-128241347                               7                         9
## >25168373-25168611                                 9                        10
## >2:25168373-25168611                              12                        12
## >25161598-25161833                                10                        11
## >24283548-24283843                                10                        10
## >7:24283548-24283843                              12                        12
## >78358469-78358619                                14                        15
## >7:128241036-1282413                              14                        15
## >2:25161598-25161833                              12                        10
## >17:78358469-7835861                              14                        14
## >31575210-31575467                                13                        14
## >24283796-24283936                                14                        13
## >7:24283796-24283936                              13                        12
## >6:31575210-31575467                              12                        13
##                      >5:10649438-10649513 11784_75BP >3611860-3611931 106_71BP
## >128241036-128241347                              14                        13
## >25168373-25168611                                16                        13
## >2:25168373-25168611                               9                        10
## >25161598-25161833                                15                        11
## >24283548-24283843                                10                        10
## >7:24283548-24283843                              11                        12
## >78358469-78358619                                13                        11
## >7:128241036-1282413                              13                        12
## >2:25161598-25161833                              12                         8
## >17:78358469-7835861                              13                         9
## >31575210-31575467                                14                         9
## >24283796-24283936                                13                        13
## >7:24283796-24283936                              11                        12
## >6:31575210-31575467                              13                        13
##                      >10:103584482-103584577 117_95BP
## >128241036-128241347                               14
## >25168373-25168611                                 15
## >2:25168373-25168611                               11
## >25161598-25161833                                 12
## >24283548-24283843                                 14
## >7:24283548-24283843                               14
## >78358469-78358619                                 14
## >7:128241036-1282413                               13
## >2:25161598-25161833                                9
## >17:78358469-7835861                                9
## >31575210-31575467                                 11
## >24283796-24283936                                 14
## >7:24283796-24283936                               12
## >6:31575210-31575467                               13
##                      >103584482-103584577 117_95BP
## >128241036-128241347                            13
## >25168373-25168611                              13
## >2:25168373-25168611                             8
## >25161598-25161833                              12
## >24283548-24283843                               9
## >7:24283548-24283843                             9
## >78358469-78358619                              16
## >7:128241036-1282413                            15
## >2:25161598-25161833                            12
## >17:78358469-7835861                            12
## >31575210-31575467                              13
## >24283796-24283936                              15
## >7:24283796-24283936                            10
## >6:31575210-31575467                            14
##                      >10649438-10649513 11784_75BP >14989629-14989930 213_301BP
## >128241036-128241347                            12                           11
## >25168373-25168611                              14                           15
## >2:25168373-25168611                             8                            8
## >25161598-25161833                              10                           10
## >24283548-24283843                              10                           12
## >7:24283548-24283843                            12                           12
## >78358469-78358619                              16                           15
## >7:128241036-1282413                            15                           17
## >2:25161598-25161833                            11                           14
## >17:78358469-7835861                            12                           16
## >31575210-31575467                              13                           15
## >24283796-24283936                              14                           15
## >7:24283796-24283936                            14                           11
## >6:31575210-31575467                            15                           15
##                      >4:3611860-3611931 106_71BP
## >128241036-128241347                          11
## >25168373-25168611                            13
## >2:25168373-25168611                           6
## >25161598-25161833                             9
## >24283548-24283843                            11
## >7:24283548-24283843                          11
## >78358469-78358619                            13
## >7:128241036-1282413                          16
## >2:25161598-25161833                          15
## >17:78358469-7835861                          13
## >31575210-31575467                            14
## >24283796-24283936                            13
## >7:24283796-24283936                          13
## >6:31575210-31575467                          13
##                      >5:131945721-131945800 2391_79BP
## >128241036-128241347                               11
## >25168373-25168611                                 10
## >2:25168373-25168611                                8
## >25161598-25161833                                 10
## >24283548-24283843                                 10
## >7:24283548-24283843                               12
## >78358469-78358619                                 16
## >7:128241036-1282413                               16
## >2:25161598-25161833                               13
## >17:78358469-7835861                               14
## >31575210-31575467                                 16
## >24283796-24283936                                 13
## >7:24283796-24283936                               13
## >6:31575210-31575467                               14
## 
## [[19]]$rowDendrogram
## 'dendrogram' with 2 branches and 20 members total, at height 22.36068 
## 
## [[19]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 30 
## 
## [[19]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[19]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[19]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[19]]$layout
## [[19]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[19]]$layout$lhei
## [1] 1.5 4.0
## 
## [[19]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[20]]
## [[20]]$rowInd
##  [1]  9  8 15 11 12  7 17  6  5 10 16  4 14 13 18  3  1  2
## 
## [[20]]$colInd
##  [1] 14  7  2 10 13  1  3  8 12  6  4 11  9  5
## 
## [[20]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[20]]$carpet
##                      >X:13044599-13044672 465_73BP
## >78358469-78358619                              10
## >7:128241036-1282413                            11
## >2:25161598-25161833                            13
## >24283796-24283936                              13
## >31575210-31575467                              12
## >17:78358469-7835861                            14
## >2:25168373-25168611                            14
## >128241036-128241347                            15
## >25168373-25168611                              12
## >7:24283796-24283936                            11
## >6:31575210-31575467                            16
## >25161598-25161833                              12
## >24283548-24283843                              11
## >7:24283548-24283843                            10
##                      >8:22055623-22055743 2879_120BP
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25161598-25161833                              11
## >24283796-24283936                                10
## >31575210-31575467                                11
## >17:78358469-7835861                              12
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25168373-25168611                                15
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
## >25161598-25161833                                12
## >24283548-24283843                                12
## >7:24283548-24283843                              11
##                      >18611255-18611340 239_85BP >112387835-112387898 195_63BP
## >78358469-78358619                             8                             8
## >7:128241036-1282413                           7                             7
## >2:25161598-25161833                          10                            10
## >24283796-24283936                            12                            12
## >31575210-31575467                            10                            10
## >17:78358469-7835861                          10                            10
## >2:25168373-25168611                          17                            17
## >128241036-128241347                          17                            17
## >25168373-25168611                            16                            16
## >7:24283796-24283936                          12                            12
## >6:31575210-31575467                          13                            13
## >25161598-25161833                            14                            14
## >24283548-24283843                            14                            14
## >7:24283548-24283843                          14                            14
##                      >112387982-112388053 195_71BP
## >78358469-78358619                               8
## >7:128241036-1282413                             7
## >2:25161598-25161833                            10
## >24283796-24283936                              12
## >31575210-31575467                              10
## >17:78358469-7835861                            10
## >2:25168373-25168611                            17
## >128241036-128241347                            17
## >25168373-25168611                              16
## >7:24283796-24283936                            12
## >6:31575210-31575467                            13
## >25161598-25161833                              14
## >24283548-24283843                              14
## >7:24283548-24283843                            14
##                      >5:131945721-131945799 2036_78BP >3412110-3412182 212_72BP
## >78358469-78358619                                 16                        15
## >7:128241036-1282413                               16                        18
## >2:25161598-25161833                               13                        13
## >24283796-24283936                                 13                        15
## >31575210-31575467                                 16                        14
## >17:78358469-7835861                               14                        14
## >2:25168373-25168611                                8                         7
## >128241036-128241347                               11                        11
## >25168373-25168611                                 10                        15
## >7:24283796-24283936                               13                        12
## >6:31575210-31575467                               14                        14
## >25161598-25161833                                 10                        11
## >24283548-24283843                                 10                        13
## >7:24283548-24283843                               12                        13
##                      >5:10649438-10649513 13490_75BP >5:865245-865502 901_257BP
## >78358469-78358619                                13                         14
## >7:128241036-1282413                              13                         14
## >2:25161598-25161833                              12                         11
## >24283796-24283936                                13                         12
## >31575210-31575467                                14                         12
## >17:78358469-7835861                              13                         10
## >2:25168373-25168611                               9                         10
## >128241036-128241347                              14                         11
## >25168373-25168611                                16                         13
## >7:24283796-24283936                              11                         14
## >6:31575210-31575467                              13                         13
## >25161598-25161833                                15                         11
## >24283548-24283843                                10                         12
## >7:24283548-24283843                              11                         13
##                      >10649438-10649513 13490_75BP
## >78358469-78358619                              16
## >7:128241036-1282413                            15
## >2:25161598-25161833                            11
## >24283796-24283936                              14
## >31575210-31575467                              13
## >17:78358469-7835861                            12
## >2:25168373-25168611                             8
## >128241036-128241347                            12
## >25168373-25168611                              14
## >7:24283796-24283936                            14
## >6:31575210-31575467                            15
## >25161598-25161833                              10
## >24283548-24283843                              10
## >7:24283548-24283843                            12
##                      >22055623-22055743 2879_120BP >18:3412110-3412182 212_72BP
## >78358469-78358619                              10                           12
## >7:128241036-1282413                            13                           14
## >2:25161598-25161833                            11                           12
## >24283796-24283936                              12                           11
## >31575210-31575467                              11                           13
## >17:78358469-7835861                            13                           12
## >2:25168373-25168611                            10                            6
## >128241036-128241347                             6                            9
## >25168373-25168611                               9                           13
## >7:24283796-24283936                            10                            9
## >6:31575210-31575467                             8                           11
## >25161598-25161833                               9                           11
## >24283548-24283843                              11                            9
## >7:24283548-24283843                            13                           10
##                      >131945721-131945799 2036_78BP >13044599-13044672 465_73BP
## >78358469-78358619                               12                          12
## >7:128241036-1282413                             12                          14
## >2:25161598-25161833                             12                          12
## >24283796-24283936                               10                          13
## >31575210-31575467                               11                          12
## >17:78358469-7835861                             11                          15
## >2:25168373-25168611                             11                          11
## >128241036-128241347                             11                           9
## >25168373-25168611                               11                           9
## >7:24283796-24283936                             10                          12
## >6:31575210-31575467                             12                          12
## >25161598-25161833                               10                           9
## >24283548-24283843                               12                          10
## >7:24283548-24283843                             10                          13
##                      >865245-865502 901_257BP >1:112387982-112388053 195_71BP
## >78358469-78358619                         15                              16
## >7:128241036-1282413                       15                              16
## >2:25161598-25161833                       10                              14
## >24283796-24283936                         13                              15
## >31575210-31575467                         14                              13
## >17:78358469-7835861                       14                              13
## >2:25168373-25168611                       12                              10
## >128241036-128241347                        9                               7
## >25168373-25168611                         10                              10
## >7:24283796-24283936                       12                              11
## >6:31575210-31575467                       13                              12
## >25161598-25161833                         11                              11
## >24283548-24283843                         10                              11
## >7:24283548-24283843                       12                              11
##                      >1:18611255-18611340 239_85BP
## >78358469-78358619                              16
## >7:128241036-1282413                            15
## >2:25161598-25161833                            15
## >24283796-24283936                              13
## >31575210-31575467                              12
## >17:78358469-7835861                            14
## >2:25168373-25168611                            10
## >128241036-128241347                             4
## >25168373-25168611                               8
## >7:24283796-24283936                            12
## >6:31575210-31575467                            12
## >25161598-25161833                              11
## >24283548-24283843                              11
## >7:24283548-24283843                             9
##                      >1:112387835-112387898 195_63BP
## >78358469-78358619                                15
## >7:128241036-1282413                              15
## >2:25161598-25161833                              15
## >24283796-24283936                                12
## >31575210-31575467                                13
## >17:78358469-7835861                              12
## >2:25168373-25168611                              10
## >128241036-128241347                               5
## >25168373-25168611                                10
## >7:24283796-24283936                              12
## >6:31575210-31575467                              11
## >25161598-25161833                                12
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## 
## [[20]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 22.36068 
## 
## [[20]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 29.93326 
## 
## [[20]]$breaks
##  [1]  4.00  4.28  4.56  4.84  5.12  5.40  5.68  5.96  6.24  6.52  6.80  7.08
## [13]  7.36  7.64  7.92  8.20  8.48  8.76  9.04  9.32  9.60  9.88 10.16 10.44
## [25] 10.72 11.00 11.28 11.56 11.84 12.12 12.40 12.68 12.96 13.24 13.52 13.80
## [37] 14.08 14.36 14.64 14.92 15.20 15.48 15.76 16.04 16.32 16.60 16.88 17.16
## [49] 17.44 17.72 18.00
## 
## [[20]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[20]]$colorTable
##      low  high   color
## 1   4.00  4.28 #FF0000
## 2   4.28  4.56 #FF0505
## 3   4.56  4.84 #FF0A0A
## 4   4.84  5.12 #FF0F0F
## 5   5.12  5.40 #FF1414
## 6   5.40  5.68 #FF1A1A
## 7   5.68  5.96 #FF1F1F
## 8   5.96  6.24 #FF2424
## 9   6.24  6.52 #FF2929
## 10  6.52  6.80 #FF2E2E
## 11  6.80  7.08 #FF3434
## 12  7.08  7.36 #FF3939
## 13  7.36  7.64 #FF3E3E
## 14  7.64  7.92 #FF4343
## 15  7.92  8.20 #FF4848
## 16  8.20  8.48 #FF4E4E
## 17  8.48  8.76 #FF5353
## 18  8.76  9.04 #FF5858
## 19  9.04  9.32 #FF5D5D
## 20  9.32  9.60 #FF6262
## 21  9.60  9.88 #FF6868
## 22  9.88 10.16 #FF6D6D
## 23 10.16 10.44 #FF7272
## 24 10.44 10.72 #FF7777
## 25 10.72 11.00 #FF7C7C
## 26 11.00 11.28 #FF8282
## 27 11.28 11.56 #FF8787
## 28 11.56 11.84 #FF8C8C
## 29 11.84 12.12 #FF9191
## 30 12.12 12.40 #FF9696
## 31 12.40 12.68 #FF9C9C
## 32 12.68 12.96 #FFA1A1
## 33 12.96 13.24 #FFA6A6
## 34 13.24 13.52 #FFABAB
## 35 13.52 13.80 #FFB0B0
## 36 13.80 14.08 #FFB6B6
## 37 14.08 14.36 #FFBBBB
## 38 14.36 14.64 #FFC0C0
## 39 14.64 14.92 #FFC5C5
## 40 14.92 15.20 #FFCACA
## 41 15.20 15.48 #FFD0D0
## 42 15.48 15.76 #FFD5D5
## 43 15.76 16.04 #FFDADA
## 44 16.04 16.32 #FFDFDF
## 45 16.32 16.60 #FFE4E4
## 46 16.60 16.88 #FFEAEA
## 47 16.88 17.16 #FFEFEF
## 48 17.16 17.44 #FFF4F4
## 49 17.44 17.72 #FFF9F9
## 50 17.72 18.00 #FFFFFF
## 
## [[20]]$layout
## [[20]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[20]]$layout$lhei
## [1] 1.5 4.0
## 
## [[20]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[21]]
## [[21]]$rowInd
##  [1]  6 10 15  2 11 16  1 21 13 20 19  3  8  5 17 14 18  7 12  9 22  4
## 
## [[21]]$colInd
##  [1]  8  3  9  5 11 12 14  7 10  4  2  6 13  1
## 
## [[21]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[21]]$carpet
##                      >4:8288864-8288951 5299_87BP
## >128241036-128241347                           15
## >2:25168373-25168611                           15
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >25161598-25161833                             13
## >25168373-25168611                             14
## >78358469-78358619                              7
## >7:128241036-1282413                            5
## >24283796-24283936                              8
## >6:31575210-31575467                           11
## >2:25161598-25161833                           12
## >7:24283796-24283936                           13
## >31575210-31575467                             11
## >17:78358469-7835861                           12
##                      >8:22055623-22055743 5609_120BP
## >128241036-128241347                              14
## >2:25168373-25168611                              15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >25161598-25161833                                12
## >25168373-25168611                                15
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >24283796-24283936                                10
## >6:31575210-31575467                              13
## >2:25161598-25161833                              11
## >7:24283796-24283936                              12
## >31575210-31575467                                11
## >17:78358469-7835861                              12
##                      >18611255-18611340 612_85BP >10:6307518-6307583 297_65BP
## >128241036-128241347                          17                           17
## >2:25168373-25168611                          17                           17
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >25161598-25161833                            14                           14
## >25168373-25168611                            16                           16
## >78358469-78358619                             8                            8
## >7:128241036-1282413                           7                            7
## >24283796-24283936                            12                           12
## >6:31575210-31575467                          13                           13
## >2:25161598-25161833                          10                           10
## >7:24283796-24283936                          12                           12
## >31575210-31575467                            10                           10
## >17:78358469-7835861                          10                           10
##                      >Y:12869914-12869975 309_61BP
## >128241036-128241347                            17
## >2:25168373-25168611                            17
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >25161598-25161833                              14
## >25168373-25168611                              16
## >78358469-78358619                               8
## >7:128241036-1282413                             7
## >24283796-24283936                              12
## >6:31575210-31575467                            13
## >2:25161598-25161833                            10
## >7:24283796-24283936                            12
## >31575210-31575467                              10
## >17:78358469-7835861                            10
##                      >22055623-22055743 5609_120BP
## >128241036-128241347                             6
## >2:25168373-25168611                            10
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >25161598-25161833                               9
## >25168373-25168611                               9
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >24283796-24283936                              12
## >6:31575210-31575467                             8
## >2:25161598-25161833                            11
## >7:24283796-24283936                            10
## >31575210-31575467                              11
## >17:78358469-7835861                            13
##                      >1:18611255-18611340 612_85BP >8288864-8288951 5299_87BP
## >128241036-128241347                             4                          6
## >2:25168373-25168611                            10                         11
## >24283548-24283843                              11                         11
## >7:24283548-24283843                             9                          9
## >25161598-25161833                              11                         12
## >25168373-25168611                               8                         11
## >78358469-78358619                              16                         15
## >7:128241036-1282413                            15                         16
## >24283796-24283936                              13                         14
## >6:31575210-31575467                            12                         12
## >2:25161598-25161833                            15                         13
## >7:24283796-24283936                            12                         11
## >31575210-31575467                              12                         14
## >17:78358469-7835861                            14                         13
##                      >12869914-12869975 309_61BP >6307518-6307583 297_65BP
## >128241036-128241347                           7                         7
## >2:25168373-25168611                          10                        10
## >24283548-24283843                            10                        10
## >7:24283548-24283843                          12                        12
## >25161598-25161833                            12                        12
## >25168373-25168611                            11                        11
## >78358469-78358619                            14                        14
## >7:128241036-1282413                          16                        16
## >24283796-24283936                            13                        13
## >6:31575210-31575467                          10                        10
## >2:25161598-25161833                          15                        15
## >7:24283796-24283936                          12                        12
## >31575210-31575467                            13                        13
## >17:78358469-7835861                          11                        11
##                      >4550782-4550844 147_62BP >17:4550782-4550844 147_62BP
## >128241036-128241347                        12                           11
## >2:25168373-25168611                        11                           10
## >24283548-24283843                          12                           11
## >7:24283548-24283843                        10                           11
## >25161598-25161833                           9                           13
## >25168373-25168611                          11                           12
## >78358469-78358619                          15                           10
## >7:128241036-1282413                        17                           10
## >24283796-24283936                          14                           10
## >6:31575210-31575467                        17                           10
## >2:25161598-25161833                        15                           15
## >7:24283796-24283936                        14                           14
## >31575210-31575467                          14                           13
## >17:78358469-7835861                        17                           13
##                      >5:10649438-10649513 18147_75BP
## >128241036-128241347                              14
## >2:25168373-25168611                               9
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >25161598-25161833                                15
## >25168373-25168611                                16
## >78358469-78358619                                13
## >7:128241036-1282413                              13
## >24283796-24283936                                13
## >6:31575210-31575467                              13
## >2:25161598-25161833                              12
## >7:24283796-24283936                              11
## >31575210-31575467                                14
## >17:78358469-7835861                              13
##                      >22:29788944-29789092 139_148BP
## >128241036-128241347                              11
## >2:25168373-25168611                              11
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >25161598-25161833                                 8
## >25168373-25168611                                 9
## >78358469-78358619                                12
## >7:128241036-1282413                              14
## >24283796-24283936                                13
## >6:31575210-31575467                              14
## >2:25161598-25161833                              11
## >7:24283796-24283936                              10
## >31575210-31575467                                11
## >17:78358469-7835861                              12
##                      >29788944-29789092 139_148BP
## >128241036-128241347                           10
## >2:25168373-25168611                           11
## >24283548-24283843                             11
## >7:24283548-24283843                           11
## >25161598-25161833                             10
## >25168373-25168611                              8
## >78358469-78358619                             11
## >7:128241036-1282413                           13
## >24283796-24283936                             11
## >6:31575210-31575467                           13
## >2:25161598-25161833                           15
## >7:24283796-24283936                           12
## >31575210-31575467                             11
## >17:78358469-7835861                           13
##                      >131945721-131945799 2085_78BP
## >128241036-128241347                             11
## >2:25168373-25168611                             11
## >24283548-24283843                               12
## >7:24283548-24283843                             10
## >25161598-25161833                               10
## >25168373-25168611                               11
## >78358469-78358619                               12
## >7:128241036-1282413                             12
## >24283796-24283936                               10
## >6:31575210-31575467                             12
## >2:25161598-25161833                             12
## >7:24283796-24283936                             10
## >31575210-31575467                               11
## >17:78358469-7835861                             11
##                      >29876340-29876455 143_115BP >5:865245-865502 1982_257BP
## >128241036-128241347                           11                          11
## >2:25168373-25168611                           11                          10
## >24283548-24283843                             12                          12
## >7:24283548-24283843                           11                          13
## >25161598-25161833                             11                          11
## >25168373-25168611                             12                          13
## >78358469-78358619                             13                          14
## >7:128241036-1282413                           14                          14
## >24283796-24283936                              9                          12
## >6:31575210-31575467                           14                          13
## >2:25161598-25161833                           13                          11
## >7:24283796-24283936                           13                          14
## >31575210-31575467                             11                          12
## >17:78358469-7835861                           13                          10
##                      >10649438-10649513 18147_75BP
## >128241036-128241347                            12
## >2:25168373-25168611                             8
## >24283548-24283843                              10
## >7:24283548-24283843                            12
## >25161598-25161833                              10
## >25168373-25168611                              14
## >78358469-78358619                              16
## >7:128241036-1282413                            15
## >24283796-24283936                              14
## >6:31575210-31575467                            15
## >2:25161598-25161833                            11
## >7:24283796-24283936                            14
## >31575210-31575467                              13
## >17:78358469-7835861                            12
##                      >5:131945721-131945799 2085_78BP >865245-865502 1982_257BP
## >128241036-128241347                               11                         9
## >2:25168373-25168611                                8                        12
## >24283548-24283843                                 10                        10
## >7:24283548-24283843                               12                        12
## >25161598-25161833                                 10                        11
## >25168373-25168611                                 10                        10
## >78358469-78358619                                 16                        15
## >7:128241036-1282413                               16                        15
## >24283796-24283936                                 13                        13
## >6:31575210-31575467                               14                        13
## >2:25161598-25161833                               13                        10
## >7:24283796-24283936                               13                        12
## >31575210-31575467                                 16                        14
## >17:78358469-7835861                               14                        14
##                      >20:29876340-29876455 143_115BP
## >128241036-128241347                              10
## >2:25168373-25168611                              12
## >24283548-24283843                                 8
## >7:24283548-24283843                              13
## >25161598-25161833                                12
## >25168373-25168611                                10
## >78358469-78358619                                14
## >7:128241036-1282413                              15
## >24283796-24283936                                14
## >6:31575210-31575467                              12
## >2:25161598-25161833                              12
## >7:24283796-24283936                              15
## >31575210-31575467                                14
## >17:78358469-7835861                              13
## 
## [[21]]$rowDendrogram
## 'dendrogram' with 2 branches and 22 members total, at height 22.36068 
## 
## [[21]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 32.24903 
## 
## [[21]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[21]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[21]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[21]]$layout
## [[21]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[21]]$layout$lhei
## [1] 1.5 4.0
## 
## [[21]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[22]]
## [[22]]$rowInd
##  [1] 12 10  3  1  6 11  7  4  2  8 13  5  9 14
## 
## [[22]]$colInd
##  [1] 10  7 14  3  8 11 12  9  5  4  6  2 13  1
## 
## [[22]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[22]]$carpet
##                      >4384227-4384295 139_68BP >131945721-131945786 682_65BP
## >24283796-24283936                           4                            10
## >7:128241036-1282413                         9                            11
## >78358469-78358619                           9                            11
## >2:25168373-25168611                        11                            12
## >128241036-128241347                         8                            11
## >25161598-25161833                          10                            12
## >25168373-25168611                          11                            13
## >24283548-24283843                          12                            10
## >7:24283548-24283843                        11                             7
## >6:31575210-31575467                        10                            10
## >7:24283796-24283936                        11                            14
## >2:25161598-25161833                        11                            10
## >31575210-31575467                          11                             9
## >17:78358469-7835861                        11                            11
##                      >5:4384227-4384295 139_68BP >4:8288864-8288951 2466_87BP
## >24283796-24283936                             9                            8
## >7:128241036-1282413                           5                            5
## >78358469-78358619                            10                            7
## >2:25168373-25168611                          14                           15
## >128241036-128241347                          12                           15
## >25161598-25161833                            15                           13
## >25168373-25168611                            14                           14
## >24283548-24283843                             9                           12
## >7:24283548-24283843                           9                           11
## >6:31575210-31575467                           9                           11
## >7:24283796-24283936                          12                           13
## >2:25161598-25161833                          13                           12
## >31575210-31575467                            12                           11
## >17:78358469-7835861                          10                           12
##                      >8:22055623-22055743 2547_120BP
## >24283796-24283936                                10
## >7:128241036-1282413                               7
## >78358469-78358619                                 7
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25161598-25161833                                12
## >25168373-25168611                                15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >6:31575210-31575467                              13
## >7:24283796-24283936                              12
## >2:25161598-25161833                              11
## >31575210-31575467                                11
## >17:78358469-7835861                              12
##                      >22055623-22055743 2547_120BP
## >24283796-24283936                              12
## >7:128241036-1282413                            13
## >78358469-78358619                              10
## >2:25168373-25168611                            10
## >128241036-128241347                             6
## >25161598-25161833                               9
## >25168373-25168611                               9
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >6:31575210-31575467                             8
## >7:24283796-24283936                            10
## >2:25161598-25161833                            11
## >31575210-31575467                              11
## >17:78358469-7835861                            13
##                      >X:13044599-13044672 420_73BP
## >24283796-24283936                              13
## >7:128241036-1282413                            11
## >78358469-78358619                              10
## >2:25168373-25168611                            14
## >128241036-128241347                            15
## >25161598-25161833                              12
## >25168373-25168611                              12
## >24283548-24283843                              11
## >7:24283548-24283843                            10
## >6:31575210-31575467                            16
## >7:24283796-24283936                            11
## >2:25161598-25161833                            13
## >31575210-31575467                              12
## >17:78358469-7835861                            14
##                      >5:10649438-10649513 9655_75BP >5:865245-865502 777_257BP
## >24283796-24283936                               13                         12
## >7:128241036-1282413                             13                         14
## >78358469-78358619                               13                         14
## >2:25168373-25168611                              9                         10
## >128241036-128241347                             14                         11
## >25161598-25161833                               15                         11
## >25168373-25168611                               16                         13
## >24283548-24283843                               10                         12
## >7:24283548-24283843                             11                         13
## >6:31575210-31575467                             13                         13
## >7:24283796-24283936                             11                         14
## >2:25161598-25161833                             12                         11
## >31575210-31575467                               14                         12
## >17:78358469-7835861                             13                         10
##                      >10649438-10649513 9655_75BP >8288864-8288951 2466_87BP
## >24283796-24283936                             14                         14
## >7:128241036-1282413                           15                         16
## >78358469-78358619                             16                         15
## >2:25168373-25168611                            8                         11
## >128241036-128241347                           12                          6
## >25161598-25161833                             10                         12
## >25168373-25168611                             14                         11
## >24283548-24283843                             10                         11
## >7:24283548-24283843                           12                          9
## >6:31575210-31575467                           15                         12
## >7:24283796-24283936                           14                         11
## >2:25161598-25161833                           11                         13
## >31575210-31575467                             13                         14
## >17:78358469-7835861                           12                         13
##                      >5:131945721-131945786 682_65BP
## >24283796-24283936                                13
## >7:128241036-1282413                              16
## >78358469-78358619                                16
## >2:25168373-25168611                               8
## >128241036-128241347                              11
## >25161598-25161833                                10
## >25168373-25168611                                10
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >6:31575210-31575467                              14
## >7:24283796-24283936                              13
## >2:25161598-25161833                              13
## >31575210-31575467                                16
## >17:78358469-7835861                              14
##                      >13044599-13044672 420_73BP >865245-865502 777_257BP
## >24283796-24283936                            13                       13
## >7:128241036-1282413                          14                       15
## >78358469-78358619                            12                       15
## >2:25168373-25168611                          11                       12
## >128241036-128241347                           9                        9
## >25161598-25161833                             9                       11
## >25168373-25168611                             9                       10
## >24283548-24283843                            10                       10
## >7:24283548-24283843                          13                       12
## >6:31575210-31575467                          12                       13
## >7:24283796-24283936                          12                       12
## >2:25161598-25161833                          12                       10
## >31575210-31575467                            12                       14
## >17:78358469-7835861                          15                       14
## 
## [[22]]$rowDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 19 
## 
## [[22]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 21.65641 
## 
## [[22]]$breaks
##  [1]  4.00  4.24  4.48  4.72  4.96  5.20  5.44  5.68  5.92  6.16  6.40  6.64
## [13]  6.88  7.12  7.36  7.60  7.84  8.08  8.32  8.56  8.80  9.04  9.28  9.52
## [25]  9.76 10.00 10.24 10.48 10.72 10.96 11.20 11.44 11.68 11.92 12.16 12.40
## [37] 12.64 12.88 13.12 13.36 13.60 13.84 14.08 14.32 14.56 14.80 15.04 15.28
## [49] 15.52 15.76 16.00
## 
## [[22]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[22]]$colorTable
##      low  high   color
## 1   4.00  4.24 #FF0000
## 2   4.24  4.48 #FF0505
## 3   4.48  4.72 #FF0A0A
## 4   4.72  4.96 #FF0F0F
## 5   4.96  5.20 #FF1414
## 6   5.20  5.44 #FF1A1A
## 7   5.44  5.68 #FF1F1F
## 8   5.68  5.92 #FF2424
## 9   5.92  6.16 #FF2929
## 10  6.16  6.40 #FF2E2E
## 11  6.40  6.64 #FF3434
## 12  6.64  6.88 #FF3939
## 13  6.88  7.12 #FF3E3E
## 14  7.12  7.36 #FF4343
## 15  7.36  7.60 #FF4848
## 16  7.60  7.84 #FF4E4E
## 17  7.84  8.08 #FF5353
## 18  8.08  8.32 #FF5858
## 19  8.32  8.56 #FF5D5D
## 20  8.56  8.80 #FF6262
## 21  8.80  9.04 #FF6868
## 22  9.04  9.28 #FF6D6D
## 23  9.28  9.52 #FF7272
## 24  9.52  9.76 #FF7777
## 25  9.76 10.00 #FF7C7C
## 26 10.00 10.24 #FF8282
## 27 10.24 10.48 #FF8787
## 28 10.48 10.72 #FF8C8C
## 29 10.72 10.96 #FF9191
## 30 10.96 11.20 #FF9696
## 31 11.20 11.44 #FF9C9C
## 32 11.44 11.68 #FFA1A1
## 33 11.68 11.92 #FFA6A6
## 34 11.92 12.16 #FFABAB
## 35 12.16 12.40 #FFB0B0
## 36 12.40 12.64 #FFB6B6
## 37 12.64 12.88 #FFBBBB
## 38 12.88 13.12 #FFC0C0
## 39 13.12 13.36 #FFC5C5
## 40 13.36 13.60 #FFCACA
## 41 13.60 13.84 #FFD0D0
## 42 13.84 14.08 #FFD5D5
## 43 14.08 14.32 #FFDADA
## 44 14.32 14.56 #FFDFDF
## 45 14.56 14.80 #FFE4E4
## 46 14.80 15.04 #FFEAEA
## 47 15.04 15.28 #FFEFEF
## 48 15.28 15.52 #FFF4F4
## 49 15.52 15.76 #FFF9F9
## 50 15.76 16.00 #FFFFFF
## 
## [[22]]$layout
## [[22]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[22]]$layout$lhei
## [1] 1.5 4.0
## 
## [[22]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[23]]
## [[23]]$rowInd
##  [1] 12  4 13  5  9 15  7  6  2 10 11 14 16  3  1 17 18  8
## 
## [[23]]$colInd
##  [1]  7 14  3  8 12 13  1 10  4  9  5  2 11  6
## 
## [[23]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[23]]$carpet
##                      >131945721-131945786 1027_65BP
## >7:128241036-1282413                             11
## >78358469-78358619                               11
## >2:25168373-25168611                             12
## >128241036-128241347                             11
## >25168373-25168611                               13
## >31575210-31575467                                9
## >17:78358469-7835861                             11
## >24283796-24283936                               10
## >6:31575210-31575467                             10
## >24283548-24283843                               10
## >7:24283548-24283843                              7
## >2:25161598-25161833                             10
## >25161598-25161833                               12
## >7:24283796-24283936                             14
##                      >20:29411394-29411458 392_64BP >18611255-18611316 367_61BP
## >7:128241036-1282413                             10                           7
## >78358469-78358619                               10                           8
## >2:25168373-25168611                             14                          17
## >128241036-128241347                             13                          17
## >25168373-25168611                               13                          16
## >31575210-31575467                                7                          10
## >17:78358469-7835861                             11                          10
## >24283796-24283936                                9                          12
## >6:31575210-31575467                              9                          13
## >24283548-24283843                               12                          14
## >7:24283548-24283843                             14                          14
## >2:25161598-25161833                             12                          10
## >25161598-25161833                               12                          14
## >7:24283796-24283936                             12                          12
##                      >4:8288864-8288951 3994_87BP
## >7:128241036-1282413                            5
## >78358469-78358619                              7
## >2:25168373-25168611                           15
## >128241036-128241347                           15
## >25168373-25168611                             14
## >31575210-31575467                             11
## >17:78358469-7835861                           12
## >24283796-24283936                              8
## >6:31575210-31575467                           11
## >24283548-24283843                             12
## >7:24283548-24283843                           11
## >2:25161598-25161833                           12
## >25161598-25161833                             13
## >7:24283796-24283936                           13
##                      >8:22055623-22055743 3993_120BP
## >7:128241036-1282413                               7
## >78358469-78358619                                 7
## >2:25168373-25168611                              15
## >128241036-128241347                              14
## >25168373-25168611                                15
## >31575210-31575467                                11
## >17:78358469-7835861                              12
## >24283796-24283936                                10
## >6:31575210-31575467                              13
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >2:25161598-25161833                              11
## >25161598-25161833                                12
## >7:24283796-24283936                              12
##                      >29411394-29411458 392_64BP
## >7:128241036-1282413                          12
## >78358469-78358619                            12
## >2:25168373-25168611                          12
## >128241036-128241347                          11
## >25168373-25168611                            11
## >31575210-31575467                            11
## >17:78358469-7835861                          12
## >24283796-24283936                            12
## >6:31575210-31575467                          14
## >24283548-24283843                             5
## >7:24283548-24283843                          10
## >2:25161598-25161833                          13
## >25161598-25161833                            13
## >7:24283796-24283936                          12
##                      >5:10649438-10649513 17948_75BP >5:865245-865502 541_257BP
## >7:128241036-1282413                              13                         14
## >78358469-78358619                                13                         14
## >2:25168373-25168611                               9                         10
## >128241036-128241347                              14                         11
## >25168373-25168611                                16                         13
## >31575210-31575467                                14                         12
## >17:78358469-7835861                              13                         10
## >24283796-24283936                                13                         12
## >6:31575210-31575467                              13                         13
## >24283548-24283843                                10                         12
## >7:24283548-24283843                              11                         13
## >2:25161598-25161833                              12                         11
## >25161598-25161833                                15                         11
## >7:24283796-24283936                              11                         14
##                      >10:125774165-125774287 162_122BP
## >7:128241036-1282413                                13
## >78358469-78358619                                  14
## >2:25168373-25168611                                11
## >128241036-128241347                                14
## >25168373-25168611                                  12
## >31575210-31575467                                  11
## >17:78358469-7835861                                10
## >24283796-24283936                                  15
## >6:31575210-31575467                                12
## >24283548-24283843                                  11
## >7:24283548-24283843                                14
## >2:25161598-25161833                                10
## >25161598-25161833                                  11
## >7:24283796-24283936                                13
##                      >10649438-10649513 17948_75BP
## >7:128241036-1282413                            15
## >78358469-78358619                              16
## >2:25168373-25168611                             8
## >128241036-128241347                            12
## >25168373-25168611                              14
## >31575210-31575467                              13
## >17:78358469-7835861                            12
## >24283796-24283936                              14
## >6:31575210-31575467                            15
## >24283548-24283843                              10
## >7:24283548-24283843                            12
## >2:25161598-25161833                            11
## >25161598-25161833                              10
## >7:24283796-24283936                            14
##                      >125774165-125774287 162_122BP
## >7:128241036-1282413                             14
## >78358469-78358619                               17
## >2:25168373-25168611                             12
## >128241036-128241347                             12
## >25168373-25168611                               15
## >31575210-31575467                               12
## >17:78358469-7835861                             10
## >24283796-24283936                               15
## >6:31575210-31575467                             15
## >24283548-24283843                               12
## >7:24283548-24283843                             11
## >2:25161598-25161833                             10
## >25161598-25161833                               12
## >7:24283796-24283936                             14
##                      >22055623-22055743 3993_120BP >65786127-65786205 136_78BP
## >7:128241036-1282413                            13                          13
## >78358469-78358619                              10                          13
## >2:25168373-25168611                            10                          11
## >128241036-128241347                             6                          10
## >25168373-25168611                               9                          10
## >31575210-31575467                              11                          12
## >17:78358469-7835861                            13                          13
## >24283796-24283936                              12                          14
## >6:31575210-31575467                             8                          13
## >24283548-24283843                              11                          11
## >7:24283548-24283843                            13                          12
## >2:25161598-25161833                            11                           8
## >25161598-25161833                               9                           8
## >7:24283796-24283936                            10                           8
##                      >11:65786127-65786205 136_78BP
## >7:128241036-1282413                             15
## >78358469-78358619                               12
## >2:25168373-25168611                              9
## >128241036-128241347                             11
## >25168373-25168611                               13
## >31575210-31575467                               14
## >17:78358469-7835861                             12
## >24283796-24283936                               11
## >6:31575210-31575467                             12
## >24283548-24283843                               10
## >7:24283548-24283843                             11
## >2:25161598-25161833                             11
## >25161598-25161833                                9
## >7:24283796-24283936                              9
##                      >1:18611255-18611316 367_61BP >8288864-8288951 3994_87BP
## >7:128241036-1282413                            15                         16
## >78358469-78358619                              16                         15
## >2:25168373-25168611                            10                         11
## >128241036-128241347                             4                          6
## >25168373-25168611                               8                         11
## >31575210-31575467                              12                         14
## >17:78358469-7835861                            14                         13
## >24283796-24283936                              13                         14
## >6:31575210-31575467                            12                         12
## >24283548-24283843                              11                         11
## >7:24283548-24283843                             9                          9
## >2:25161598-25161833                            15                         13
## >25161598-25161833                              11                         12
## >7:24283796-24283936                            12                         11
##                      >865245-865502 541_257BP >5:131945721-131945786 1027_65BP
## >7:128241036-1282413                       15                               16
## >78358469-78358619                         15                               16
## >2:25168373-25168611                       12                                8
## >128241036-128241347                        9                               11
## >25168373-25168611                         10                               10
## >31575210-31575467                         14                               16
## >17:78358469-7835861                       14                               14
## >24283796-24283936                         13                               13
## >6:31575210-31575467                       13                               14
## >24283548-24283843                         10                               10
## >7:24283548-24283843                       12                               12
## >2:25161598-25161833                       10                               13
## >25161598-25161833                         11                               10
## >7:24283796-24283936                       12                               13
## 
## [[23]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 22.36068 
## 
## [[23]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 25.27845 
## 
## [[23]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[23]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[23]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[23]]$layout
## [[23]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[23]]$layout$lhei
## [1] 1.5 4.0
## 
## [[23]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[24]]
## [[24]]$rowInd
##  [1]  8 12  7 13  2  9 14  1 11 17  6 18  3  4 10 15 16  5
## 
## [[24]]$colInd
##  [1] 14  7  2 13  1 10  8  3  9  5 11 12  6  4
## 
## [[24]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[24]]$carpet
##                      >9:31321373-31321440 119_67BP
## >78358469-78358619                               8
## >7:128241036-1282413                             9
## >2:25161598-25161833                            10
## >31575210-31575467                              10
## >17:78358469-7835861                             9
## >24283796-24283936                               8
## >128241036-128241347                            11
## >2:25168373-25168611                            13
## >24283548-24283843                              11
## >7:24283548-24283843                            12
## >25161598-25161833                              11
## >25168373-25168611                              12
## >7:24283796-24283936                            11
## >6:31575210-31575467                            10
##                      >131945721-131945786 780_65BP
## >78358469-78358619                              11
## >7:128241036-1282413                            11
## >2:25161598-25161833                            10
## >31575210-31575467                               9
## >17:78358469-7835861                            11
## >24283796-24283936                              10
## >128241036-128241347                            11
## >2:25168373-25168611                            12
## >24283548-24283843                              10
## >7:24283548-24283843                             7
## >25161598-25161833                              12
## >25168373-25168611                              13
## >7:24283796-24283936                            14
## >6:31575210-31575467                            10
##                      >8:22055623-22055743 3376_120BP
## >78358469-78358619                                 7
## >7:128241036-1282413                               7
## >2:25161598-25161833                              11
## >31575210-31575467                                11
## >17:78358469-7835861                              12
## >24283796-24283936                                10
## >128241036-128241347                              14
## >2:25168373-25168611                              15
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >25161598-25161833                                12
## >25168373-25168611                                15
## >7:24283796-24283936                              12
## >6:31575210-31575467                              13
##                      >18611255-18611324 366_69BP >10:6307518-6307583 387_65BP
## >78358469-78358619                             8                            8
## >7:128241036-1282413                           7                            7
## >2:25161598-25161833                          10                           10
## >31575210-31575467                            10                           10
## >17:78358469-7835861                          10                           10
## >24283796-24283936                            12                           12
## >128241036-128241347                          17                           17
## >2:25168373-25168611                          17                           17
## >24283548-24283843                            14                           14
## >7:24283548-24283843                          14                           14
## >25161598-25161833                            14                           14
## >25168373-25168611                            16                           16
## >7:24283796-24283936                          12                           12
## >6:31575210-31575467                          13                           13
##                      >Y:12869910-12869975 374_65BP
## >78358469-78358619                               8
## >7:128241036-1282413                             7
## >2:25161598-25161833                            10
## >31575210-31575467                              10
## >17:78358469-7835861                            10
## >24283796-24283936                              12
## >128241036-128241347                            17
## >2:25168373-25168611                            17
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >25161598-25161833                              14
## >25168373-25168611                              16
## >7:24283796-24283936                            12
## >6:31575210-31575467                            13
##                      >22055623-22055743 3376_120BP
## >78358469-78358619                              10
## >7:128241036-1282413                            13
## >2:25161598-25161833                            11
## >31575210-31575467                              11
## >17:78358469-7835861                            13
## >24283796-24283936                              12
## >128241036-128241347                             6
## >2:25168373-25168611                            10
## >24283548-24283843                              11
## >7:24283548-24283843                            13
## >25161598-25161833                               9
## >25168373-25168611                               9
## >7:24283796-24283936                            10
## >6:31575210-31575467                             8
##                      >1:18611255-18611324 366_69BP >12869910-12869975 374_65BP
## >78358469-78358619                              16                          14
## >7:128241036-1282413                            15                          16
## >2:25161598-25161833                            15                          15
## >31575210-31575467                              12                          13
## >17:78358469-7835861                            14                          11
## >24283796-24283936                              13                          13
## >128241036-128241347                             4                           7
## >2:25168373-25168611                            10                          10
## >24283548-24283843                              11                          10
## >7:24283548-24283843                             9                          12
## >25161598-25161833                              11                          12
## >25168373-25168611                               8                          11
## >7:24283796-24283936                            12                          12
## >6:31575210-31575467                            12                          10
##                      >6307518-6307583 387_65BP >5:131945721-131945786 780_65BP
## >78358469-78358619                          14                              16
## >7:128241036-1282413                        16                              16
## >2:25161598-25161833                        15                              13
## >31575210-31575467                          13                              16
## >17:78358469-7835861                        11                              14
## >24283796-24283936                          13                              13
## >128241036-128241347                         7                              11
## >2:25168373-25168611                        10                               8
## >24283548-24283843                          10                              10
## >7:24283548-24283843                        12                              12
## >25161598-25161833                          12                              10
## >25168373-25168611                          11                              10
## >7:24283796-24283936                        12                              13
## >6:31575210-31575467                        10                              14
##                      >865245-865502 2334_257BP >17:43665375-43665443 115_68BP
## >78358469-78358619                          15                             13
## >7:128241036-1282413                        15                             17
## >2:25161598-25161833                        10                             12
## >31575210-31575467                          14                             14
## >17:78358469-7835861                        14                             15
## >24283796-24283936                          13                             15
## >128241036-128241347                         9                             11
## >2:25168373-25168611                        12                             12
## >24283548-24283843                          10                             13
## >7:24283548-24283843                        12                             12
## >25161598-25161833                          11                              9
## >25168373-25168611                          10                              9
## >7:24283796-24283936                        12                             12
## >6:31575210-31575467                        13                             14
##                      >5:865245-865502 2334_257BP >10649438-10649513 8206_75BP
## >78358469-78358619                            14                           16
## >7:128241036-1282413                          14                           15
## >2:25161598-25161833                          11                           11
## >31575210-31575467                            12                           13
## >17:78358469-7835861                          10                           12
## >24283796-24283936                            12                           14
## >128241036-128241347                          11                           12
## >2:25168373-25168611                          10                            8
## >24283548-24283843                            12                           10
## >7:24283548-24283843                          13                           12
## >25161598-25161833                            11                           10
## >25168373-25168611                            13                           14
## >7:24283796-24283936                          14                           14
## >6:31575210-31575467                          13                           15
##                      >31321373-31321440 119_67BP >43665375-43665443 115_68BP
## >78358469-78358619                            12                          12
## >7:128241036-1282413                          13                          13
## >2:25161598-25161833                          12                          11
## >31575210-31575467                            13                          14
## >17:78358469-7835861                          12                          11
## >24283796-24283936                            11                          12
## >128241036-128241347                          13                          13
## >2:25168373-25168611                          10                           7
## >24283548-24283843                            10                          10
## >7:24283548-24283843                           6                          11
## >25161598-25161833                            12                          12
## >25168373-25168611                            14                          15
## >7:24283796-24283936                          13                          11
## >6:31575210-31575467                          16                          11
##                      >5:10649438-10649513 8206_75BP
## >78358469-78358619                               13
## >7:128241036-1282413                             13
## >2:25161598-25161833                             12
## >31575210-31575467                               14
## >17:78358469-7835861                             13
## >24283796-24283936                               13
## >128241036-128241347                             14
## >2:25168373-25168611                              9
## >24283548-24283843                               10
## >7:24283548-24283843                             11
## >25161598-25161833                               15
## >25168373-25168611                               16
## >7:24283796-24283936                             11
## >6:31575210-31575467                             13
## 
## [[24]]$rowDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 22.36068 
## 
## [[24]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 28.30194 
## 
## [[24]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[24]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[24]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[24]]$layout
## [[24]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[24]]$layout$lhei
## [1] 1.5 4.0
## 
## [[24]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[25]]
## [[25]]$rowInd
##  [1] 27  8 16 21 37 19 15 25  1 32 41  3 38 10  2 36 12 17 26 24 28 13  9 23  5
## [26] 31 40 20 42 30 29 22 44 34 46  6  7 33 11  4 39 43 18 45 35 14
## 
## [[25]]$colInd
##  [1]  4 13  1 14 10  7  3 11  8 12  9  5  2  6
## 
## [[25]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[25]]$carpet
##                      >130916242-130916335 212_93BP
## >6:31575210-31575467                            13
## >31575210-31575467                              15
## >17:78358469-7835861                            13
## >78358469-78358619                              15
## >24283796-24283936                              15
## >7:128241036-1282413                            13
## >2:25168373-25168611                            12
## >25161598-25161833                              12
## >128241036-128241347                            14
## >25168373-25168611                              15
## >24283548-24283843                              14
## >7:24283548-24283843                            14
## >2:25161598-25161833                            10
## >7:24283796-24283936                            13
##                      >16:70251562-70251701 243_139BP
## >6:31575210-31575467                              17
## >31575210-31575467                                16
## >17:78358469-7835861                              15
## >78358469-78358619                                16
## >24283796-24283936                                16
## >7:128241036-1282413                              16
## >2:25168373-25168611                              10
## >25161598-25161833                                 9
## >128241036-128241347                              12
## >25168373-25168611                                15
## >24283548-24283843                                13
## >7:24283548-24283843                              12
## >2:25161598-25161833                              13
## >7:24283796-24283936                              12
##                      >6:39792402-39792463 228_61BP
## >6:31575210-31575467                            17
## >31575210-31575467                              17
## >17:78358469-7835861                            16
## >78358469-78358619                              16
## >24283796-24283936                              16
## >7:128241036-1282413                            17
## >2:25168373-25168611                            10
## >25161598-25161833                              10
## >128241036-128241347                            13
## >25168373-25168611                              14
## >24283548-24283843                              14
## >7:24283548-24283843                            12
## >2:25161598-25161833                            14
## >7:24283796-24283936                            14
##                      >9:36136741-36136851 380_110BP
## >6:31575210-31575467                             14
## >31575210-31575467                               14
## >17:78358469-7835861                             15
## >78358469-78358619                               14
## >24283796-24283936                               14
## >7:128241036-1282413                             16
## >2:25168373-25168611                              7
## >25161598-25161833                               10
## >128241036-128241347                             10
## >25168373-25168611                               11
## >24283548-24283843                               12
## >7:24283548-24283843                             13
## >2:25161598-25161833                             10
## >7:24283796-24283936                             12
##                      >32347230-32347346 160_116BP
## >6:31575210-31575467                           11
## >31575210-31575467                             14
## >17:78358469-7835861                           15
## >78358469-78358619                             14
## >24283796-24283936                             14
## >7:128241036-1282413                           15
## >2:25168373-25168611                            8
## >25161598-25161833                              9
## >128241036-128241347                           10
## >25168373-25168611                             11
## >24283548-24283843                             13
## >7:24283548-24283843                           13
## >2:25161598-25161833                           12
## >7:24283796-24283936                           14
##                      >8:66712550-66712702 3980_152BP
## >6:31575210-31575467                              13
## >31575210-31575467                                14
## >17:78358469-7835861                              14
## >78358469-78358619                                15
## >24283796-24283936                                13
## >7:128241036-1282413                              16
## >2:25168373-25168611                               9
## >25161598-25161833                                10
## >128241036-128241347                               9
## >25168373-25168611                                10
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >2:25161598-25161833                              13
## >7:24283796-24283936                              13
##                      >5:131945721-131945786 511_65BP
## >6:31575210-31575467                              14
## >31575210-31575467                                16
## >17:78358469-7835861                              14
## >78358469-78358619                                16
## >24283796-24283936                                13
## >7:128241036-1282413                              16
## >2:25168373-25168611                               8
## >25161598-25161833                                10
## >128241036-128241347                              11
## >25168373-25168611                                10
## >24283548-24283843                                10
## >7:24283548-24283843                              12
## >2:25161598-25161833                              13
## >7:24283796-24283936                              13
##                      >10649439-10649513 1822_74BP
## >6:31575210-31575467                           15
## >31575210-31575467                             13
## >17:78358469-7835861                           12
## >78358469-78358619                             16
## >24283796-24283936                             14
## >7:128241036-1282413                           15
## >2:25168373-25168611                            8
## >25161598-25161833                             10
## >128241036-128241347                           12
## >25168373-25168611                             14
## >24283548-24283843                             10
## >7:24283548-24283843                           12
## >2:25161598-25161833                           11
## >7:24283796-24283936                           14
##                      >1:164321420-164321491 119_71BP
## >6:31575210-31575467                              15
## >31575210-31575467                                15
## >17:78358469-7835861                              13
## >78358469-78358619                                16
## >24283796-24283936                                15
## >7:128241036-1282413                              15
## >2:25168373-25168611                               8
## >25161598-25161833                                12
## >128241036-128241347                              11
## >25168373-25168611                                12
## >24283548-24283843                                12
## >7:24283548-24283843                              14
## >2:25161598-25161833                              12
## >7:24283796-24283936                              15
##                      >15786192-15786281 179_89BP >66712550-66712702 3980_152BP
## >6:31575210-31575467                          13                            13
## >31575210-31575467                            14                            15
## >17:78358469-7835861                          14                            14
## >78358469-78358619                            16                            16
## >24283796-24283936                            16                            16
## >7:128241036-1282413                          16                            17
## >2:25168373-25168611                           7                             7
## >25161598-25161833                            11                            12
## >128241036-128241347                          13                            12
## >25168373-25168611                            12                            13
## >24283548-24283843                            11                            12
## >7:24283548-24283843                          15                            12
## >2:25161598-25161833                          12                            12
## >7:24283796-24283936                          14                            13
##                      >10:32347230-32347346 160_116BP
## >6:31575210-31575467                              15
## >31575210-31575467                                15
## >17:78358469-7835861                              14
## >78358469-78358619                                17
## >24283796-24283936                                15
## >7:128241036-1282413                              14
## >2:25168373-25168611                              10
## >25161598-25161833                                11
## >128241036-128241347                              13
## >25168373-25168611                                11
## >24283548-24283843                                12
## >7:24283548-24283843                              11
## >2:25161598-25161833                              13
## >7:24283796-24283936                              11
##                      >36136741-36136851 380_110BP
## >6:31575210-31575467                           14
## >31575210-31575467                             15
## >17:78358469-7835861                           14
## >78358469-78358619                             15
## >24283796-24283936                             15
## >7:128241036-1282413                           15
## >2:25168373-25168611                           10
## >25161598-25161833                             10
## >128241036-128241347                           12
## >25168373-25168611                             13
## >24283548-24283843                             12
## >7:24283548-24283843                           13
## >2:25161598-25161833                           11
## >7:24283796-24283936                           12
##                      >17:15786192-15786281 179_89BP
## >6:31575210-31575467                             15
## >31575210-31575467                               14
## >17:78358469-7835861                             14
## >78358469-78358619                               15
## >24283796-24283936                               16
## >7:128241036-1282413                             16
## >2:25168373-25168611                             10
## >25161598-25161833                               11
## >128241036-128241347                             12
## >25168373-25168611                               11
## >24283548-24283843                               10
## >7:24283548-24283843                             13
## >2:25161598-25161833                             12
## >7:24283796-24283936                             13
##                      >1:240093617-240093698 148_81BP
## >6:31575210-31575467                              16
## >31575210-31575467                                15
## >17:78358469-7835861                              14
## >78358469-78358619                                16
## >24283796-24283936                                15
## >7:128241036-1282413                              16
## >2:25168373-25168611                               8
## >25161598-25161833                                 9
## >128241036-128241347                              12
## >25168373-25168611                                12
## >24283548-24283843                                12
## >7:24283548-24283843                              12
## >2:25161598-25161833                              13
## >7:24283796-24283936                              12
##                      >30812217-30812293 326_76BP >4:8288864-8288951 810_87BP
## >6:31575210-31575467                          15                          11
## >31575210-31575467                            14                          11
## >17:78358469-7835861                          13                          12
## >78358469-78358619                            17                           7
## >24283796-24283936                            15                           8
## >7:128241036-1282413                          17                           5
## >2:25168373-25168611                           8                          15
## >25161598-25161833                            11                          13
## >128241036-128241347                          12                          15
## >25168373-25168611                            12                          14
## >24283548-24283843                            12                          12
## >7:24283548-24283843                          13                          11
## >2:25161598-25161833                          11                          12
## >7:24283796-24283936                          12                          13
##                      >8:22055623-22055726 220_103BP
## >6:31575210-31575467                             13
## >31575210-31575467                               11
## >17:78358469-7835861                             12
## >78358469-78358619                                7
## >24283796-24283936                               10
## >7:128241036-1282413                              7
## >2:25168373-25168611                             15
## >25161598-25161833                               12
## >128241036-128241347                             14
## >25168373-25168611                               15
## >24283548-24283843                               12
## >7:24283548-24283843                             11
## >2:25161598-25161833                             11
## >7:24283796-24283936                             12
##                      >122261613-122261700 844_87BP
## >6:31575210-31575467                            16
## >31575210-31575467                              11
## >17:78358469-7835861                            13
## >78358469-78358619                              12
## >24283796-24283936                               7
## >7:128241036-1282413                            11
## >2:25168373-25168611                            12
## >25161598-25161833                              13
## >128241036-128241347                            13
## >25168373-25168611                              13
## >24283548-24283843                              11
## >7:24283548-24283843                            10
## >2:25161598-25161833                            13
## >7:24283796-24283936                            13
##                      >100372360-100372458 518_98BP
## >6:31575210-31575467                            12
## >31575210-31575467                              10
## >17:78358469-7835861                            10
## >78358469-78358619                              12
## >24283796-24283936                               7
## >7:128241036-1282413                             8
## >2:25168373-25168611                            10
## >25161598-25161833                              13
## >128241036-128241347                            11
## >25168373-25168611                              13
## >24283548-24283843                               8
## >7:24283548-24283843                             8
## >2:25161598-25161833                            11
## >7:24283796-24283936                            13
##                      >131945721-131945786 511_65BP
## >6:31575210-31575467                            10
## >31575210-31575467                               9
## >17:78358469-7835861                            11
## >78358469-78358619                              11
## >24283796-24283936                              10
## >7:128241036-1282413                            11
## >2:25168373-25168611                            12
## >25161598-25161833                              12
## >128241036-128241347                            11
## >25168373-25168611                              13
## >24283548-24283843                              10
## >7:24283548-24283843                             7
## >2:25161598-25161833                            10
## >7:24283796-24283936                            14
##                      >4:122261613-122261700 844_87BP
## >6:31575210-31575467                               7
## >31575210-31575467                                 9
## >17:78358469-7835861                               8
## >78358469-78358619                                10
## >24283796-24283936                                 8
## >7:128241036-1282413                              11
## >2:25168373-25168611                              11
## >25161598-25161833                                10
## >128241036-128241347                               4
## >25168373-25168611                                 9
## >24283548-24283843                                 9
## >7:24283548-24283843                              12
## >2:25161598-25161833                              10
## >7:24283796-24283936                              10
##                      >17:13254784-13254854 276_70BP >X:5359719-5359783 196_64BP
## >6:31575210-31575467                             10                           8
## >31575210-31575467                               10                          12
## >17:78358469-7835861                             11                          11
## >78358469-78358619                                9                           9
## >24283796-24283936                               12                          11
## >7:128241036-1282413                             11                          11
## >2:25168373-25168611                             11                          10
## >25161598-25161833                                9                          13
## >128241036-128241347                             10                          11
## >25168373-25168611                                9                          11
## >24283548-24283843                               13                          12
## >7:24283548-24283843                             13                          13
## >2:25161598-25161833                              8                          11
## >7:24283796-24283936                              9                          10
##                      >12:100372360-100372458 518_98BP
## >6:31575210-31575467                               10
## >31575210-31575467                                 11
## >17:78358469-7835861                               13
## >78358469-78358619                                  7
## >24283796-24283936                                 11
## >7:128241036-1282413                               12
## >2:25168373-25168611                               13
## >25161598-25161833                                 11
## >128241036-128241347                               13
## >25168373-25168611                                 12
## >24283548-24283843                                  9
## >7:24283548-24283843                               12
## >2:25161598-25161833                               13
## >7:24283796-24283936                               10
##                      >14989693-14989865 116_172BP >5359719-5359783 196_64BP
## >6:31575210-31575467                           14                        12
## >31575210-31575467                             11                         7
## >17:78358469-7835861                           13                        11
## >78358469-78358619                             10                        13
## >24283796-24283936                             13                        10
## >7:128241036-1282413                           14                        10
## >2:25168373-25168611                           11                        12
## >25161598-25161833                             10                         8
## >128241036-128241347                           14                         9
## >25168373-25168611                             14                        11
## >24283548-24283843                             11                        10
## >7:24283548-24283843                           12                        12
## >2:25161598-25161833                           10                         9
## >7:24283796-24283936                            9                         9
##                      >9:76145-76236 360_91BP >68354257-68354348 360_91BP
## >6:31575210-31575467                      12                          12
## >31575210-31575467                        10                          10
## >17:78358469-7835861                      13                          13
## >78358469-78358619                        10                          10
## >24283796-24283936                        11                          11
## >7:128241036-1282413                      11                          11
## >2:25168373-25168611                      11                          11
## >25161598-25161833                        10                          10
## >128241036-128241347                       9                           9
## >25168373-25168611                         9                           9
## >24283548-24283843                         9                           9
## >7:24283548-24283843                      11                          11
## >2:25161598-25161833                      13                          13
## >7:24283796-24283936                       9                           9
##                      >138508460-138508543 879_83BP >13254784-13254854 276_70BP
## >6:31575210-31575467                            13                          12
## >31575210-31575467                               8                           8
## >17:78358469-7835861                            10                           9
## >78358469-78358619                              10                          10
## >24283796-24283936                              11                          10
## >7:128241036-1282413                            12                          11
## >2:25168373-25168611                            14                          11
## >25161598-25161833                              12                          12
## >128241036-128241347                            12                          10
## >25168373-25168611                              11                          11
## >24283548-24283843                              10                          10
## >7:24283548-24283843                            11                          12
## >2:25161598-25161833                            13                          11
## >7:24283796-24283936                            11                          12
##                      >9:68354257-68354348 360_91BP >76145-76236 360_91BP
## >6:31575210-31575467                            11                    11
## >31575210-31575467                              10                    10
## >17:78358469-7835861                            11                    11
## >78358469-78358619                              10                    10
## >24283796-24283936                              10                    10
## >7:128241036-1282413                            10                    10
## >2:25168373-25168611                            12                    12
## >25161598-25161833                              12                    12
## >128241036-128241347                            12                    12
## >25168373-25168611                              12                    12
## >24283548-24283843                              10                    10
## >7:24283548-24283843                            13                    13
## >2:25161598-25161833                            10                    10
## >7:24283796-24283936                            10                    10
##                      >22055623-22055726 220_103BP >8288864-8288951 810_87BP
## >6:31575210-31575467                           13                        12
## >31575210-31575467                             12                        14
## >17:78358469-7835861                           14                        13
## >78358469-78358619                             14                        15
## >24283796-24283936                             12                        14
## >7:128241036-1282413                           14                        16
## >2:25168373-25168611                            9                        11
## >25161598-25161833                             12                        12
## >128241036-128241347                            9                         6
## >25168373-25168611                              9                        11
## >24283548-24283843                              9                        11
## >7:24283548-24283843                            9                         9
## >2:25161598-25161833                           14                        13
## >7:24283796-24283936                           12                        11
##                      >15:80403871-80403944 491_73BP
## >6:31575210-31575467                             13
## >31575210-31575467                               11
## >17:78358469-7835861                             11
## >78358469-78358619                               14
## >24283796-24283936                               14
## >7:128241036-1282413                             14
## >2:25168373-25168611                             10
## >25161598-25161833                               10
## >128241036-128241347                             10
## >25168373-25168611                               11
## >24283548-24283843                                9
## >7:24283548-24283843                             13
## >2:25161598-25161833                             11
## >7:24283796-24283936                             13
##                      >16:14989693-14989865 116_172BP
## >6:31575210-31575467                              12
## >31575210-31575467                                11
## >17:78358469-7835861                              14
## >78358469-78358619                                14
## >24283796-24283936                                14
## >7:128241036-1282413                              14
## >2:25168373-25168611                              13
## >25161598-25161833                                10
## >128241036-128241347                              11
## >25168373-25168611                                 9
## >24283548-24283843                                11
## >7:24283548-24283843                              13
## >2:25161598-25161833                              11
## >7:24283796-24283936                              13
##                      >164321420-164321491 119_71BP
## >6:31575210-31575467                            10
## >31575210-31575467                              12
## >17:78358469-7835861                            11
## >78358469-78358619                              10
## >24283796-24283936                              11
## >7:128241036-1282413                            10
## >2:25168373-25168611                             8
## >25161598-25161833                              12
## >128241036-128241347                             9
## >25168373-25168611                              12
## >24283548-24283843                               9
## >7:24283548-24283843                             9
## >2:25161598-25161833                             9
## >7:24283796-24283936                            11
##                      >3:138508460-138508543 879_83BP
## >6:31575210-31575467                              11
## >31575210-31575467                                11
## >17:78358469-7835861                               9
## >78358469-78358619                                11
## >24283796-24283936                                13
## >7:128241036-1282413                              11
## >2:25168373-25168611                              10
## >25161598-25161833                                13
## >128241036-128241347                              11
## >25168373-25168611                                15
## >24283548-24283843                                10
## >7:24283548-24283843                              11
## >2:25161598-25161833                               9
## >7:24283796-24283936                               9
##                      >11:130916242-130916335 212_93BP
## >6:31575210-31575467                               11
## >31575210-31575467                                 13
## >17:78358469-7835861                               11
## >78358469-78358619                                 12
## >24283796-24283936                                 11
## >7:128241036-1282413                               10
## >2:25168373-25168611                               11
## >25161598-25161833                                 13
## >128241036-128241347                               13
## >25168373-25168611                                 15
## >24283548-24283843                                 12
## >7:24283548-24283843                                8
## >2:25161598-25161833                                9
## >7:24283796-24283936                               12
##                      >39792402-39792463 228_61BP >70251562-70251701 243_139BP
## >6:31575210-31575467                          12                           12
## >31575210-31575467                            13                           12
## >17:78358469-7835861                          12                           13
## >78358469-78358619                            13                           13
## >24283796-24283936                            11                           14
## >7:128241036-1282413                          11                           14
## >2:25168373-25168611                          11                            6
## >25161598-25161833                            14                           10
## >128241036-128241347                          12                           11
## >25168373-25168611                            12                           11
## >24283548-24283843                            11                           10
## >7:24283548-24283843                          11                           13
## >2:25161598-25161833                          10                           10
## >7:24283796-24283936                          13                           12
##                      >8:30812217-30812293 326_76BP >80403871-80403944 491_73BP
## >6:31575210-31575467                            14                          13
## >31575210-31575467                              12                          14
## >17:78358469-7835861                            10                          14
## >78358469-78358619                              13                          14
## >24283796-24283936                              14                          12
## >7:128241036-1282413                            14                          14
## >2:25168373-25168611                             6                           8
## >25161598-25161833                              11                          14
## >128241036-128241347                            12                          12
## >25168373-25168611                              13                          13
## >24283548-24283843                              11                          10
## >7:24283548-24283843                            12                          12
## >2:25161598-25161833                            11                          14
## >7:24283796-24283936                            10                          10
##                      >240093617-240093698 148_81BP
## >6:31575210-31575467                            14
## >31575210-31575467                              12
## >17:78358469-7835861                            12
## >78358469-78358619                              12
## >24283796-24283936                              11
## >7:128241036-1282413                            13
## >2:25168373-25168611                             8
## >25161598-25161833                              13
## >128241036-128241347                            12
## >25168373-25168611                              15
## >24283548-24283843                              10
## >7:24283548-24283843                            10
## >2:25161598-25161833                            11
## >7:24283796-24283936                            11
##                      >5:10649439-10649513 1822_74BP
## >6:31575210-31575467                             14
## >31575210-31575467                               12
## >17:78358469-7835861                             12
## >78358469-78358619                               12
## >24283796-24283936                               11
## >7:128241036-1282413                             13
## >2:25168373-25168611                              7
## >25161598-25161833                               14
## >128241036-128241347                             13
## >25168373-25168611                               16
## >24283548-24283843                               10
## >7:24283548-24283843                             10
## >2:25161598-25161833                             11
## >7:24283796-24283936                             11
## 
## [[25]]$rowDendrogram
## 'dendrogram' with 2 branches and 46 members total, at height 22.97825 
## 
## [[25]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 36.40055 
## 
## [[25]]$breaks
##  [1]  4.00  4.26  4.52  4.78  5.04  5.30  5.56  5.82  6.08  6.34  6.60  6.86
## [13]  7.12  7.38  7.64  7.90  8.16  8.42  8.68  8.94  9.20  9.46  9.72  9.98
## [25] 10.24 10.50 10.76 11.02 11.28 11.54 11.80 12.06 12.32 12.58 12.84 13.10
## [37] 13.36 13.62 13.88 14.14 14.40 14.66 14.92 15.18 15.44 15.70 15.96 16.22
## [49] 16.48 16.74 17.00
## 
## [[25]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[25]]$colorTable
##      low  high   color
## 1   4.00  4.26 #FF0000
## 2   4.26  4.52 #FF0505
## 3   4.52  4.78 #FF0A0A
## 4   4.78  5.04 #FF0F0F
## 5   5.04  5.30 #FF1414
## 6   5.30  5.56 #FF1A1A
## 7   5.56  5.82 #FF1F1F
## 8   5.82  6.08 #FF2424
## 9   6.08  6.34 #FF2929
## 10  6.34  6.60 #FF2E2E
## 11  6.60  6.86 #FF3434
## 12  6.86  7.12 #FF3939
## 13  7.12  7.38 #FF3E3E
## 14  7.38  7.64 #FF4343
## 15  7.64  7.90 #FF4848
## 16  7.90  8.16 #FF4E4E
## 17  8.16  8.42 #FF5353
## 18  8.42  8.68 #FF5858
## 19  8.68  8.94 #FF5D5D
## 20  8.94  9.20 #FF6262
## 21  9.20  9.46 #FF6868
## 22  9.46  9.72 #FF6D6D
## 23  9.72  9.98 #FF7272
## 24  9.98 10.24 #FF7777
## 25 10.24 10.50 #FF7C7C
## 26 10.50 10.76 #FF8282
## 27 10.76 11.02 #FF8787
## 28 11.02 11.28 #FF8C8C
## 29 11.28 11.54 #FF9191
## 30 11.54 11.80 #FF9696
## 31 11.80 12.06 #FF9C9C
## 32 12.06 12.32 #FFA1A1
## 33 12.32 12.58 #FFA6A6
## 34 12.58 12.84 #FFABAB
## 35 12.84 13.10 #FFB0B0
## 36 13.10 13.36 #FFB6B6
## 37 13.36 13.62 #FFBBBB
## 38 13.62 13.88 #FFC0C0
## 39 13.88 14.14 #FFC5C5
## 40 14.14 14.40 #FFCACA
## 41 14.40 14.66 #FFD0D0
## 42 14.66 14.92 #FFD5D5
## 43 14.92 15.18 #FFDADA
## 44 15.18 15.44 #FFDFDF
## 45 15.44 15.70 #FFE4E4
## 46 15.70 15.96 #FFEAEA
## 47 15.96 16.22 #FFEFEF
## 48 16.22 16.48 #FFF4F4
## 49 16.48 16.74 #FFF9F9
## 50 16.74 17.00 #FFFFFF
## 
## [[25]]$layout
## [[25]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[25]]$layout$lhei
## [1] 1.5 4.0
## 
## [[25]]$layout$lwid
## [1] 1.5 4.0
## 
## 
## 
## [[26]]
## [[26]]$rowInd
##  [1] 11  7  3 13  1 10 12 14  9  6  2  4  8  5
## 
## [[26]]$colInd
##  [1]  9 10  7  5 12 11  4  8 14  6  3 13  1  2
## 
## [[26]]$call
## heatmap.2(x = adist(seq, amp), scale = "none", col = colfunc(50), 
##     trace = "none", margins = c(15, 20), main = names(oft2)[z])
## 
## [[26]]$carpet
##                      >54011707-54011774 169_67BP >7:45596896-45596960 127_64BP
## >24283548-24283843                            11                             7
## >24283796-24283936                            10                            14
## >7:128241036-1282413                          11                            14
## >7:24283548-24283843                          13                            11
## >25168373-25168611                            10                            12
## >25161598-25161833                            10                            12
## >6:31575210-31575467                           8                            12
## >128241036-128241347                           7                            10
## >78358469-78358619                             7                            10
## >7:24283796-24283936                           9                            10
## >2:25168373-25168611                          10                             9
## >31575210-31575467                            10                            13
## >17:78358469-7835861                          12                            12
## >2:25161598-25161833                          10                            13
##                      >15:26275973-26276063 226_90BP >55273510-55273577 140_67BP
## >24283548-24283843                               10                          10
## >24283796-24283936                                9                          10
## >7:128241036-1282413                             10                          11
## >7:24283548-24283843                             10                          13
## >25168373-25168611                               13                          10
## >25161598-25161833                               12                          12
## >6:31575210-31575467                              8                           8
## >128241036-128241347                             10                          10
## >78358469-78358619                               11                          12
## >7:24283796-24283936                             12                          14
## >2:25168373-25168611                             12                          13
## >31575210-31575467                               13                          12
## >17:78358469-7835861                             12                          10
## >2:25161598-25161833                             14                          13
##                      >10:54011707-54011774 169_67BP >45596896-45596960 127_64BP
## >24283548-24283843                               11                          11
## >24283796-24283936                                9                          11
## >7:128241036-1282413                             11                          13
## >7:24283548-24283843                             11                          13
## >25168373-25168611                                8                          10
## >25161598-25161833                               11                          10
## >6:31575210-31575467                             13                          10
## >128241036-128241347                             10                          10
## >78358469-78358619                               11                          12
## >7:24283796-24283936                             11                          11
## >2:25168373-25168611                             12                          13
## >31575210-31575467                               13                          11
## >17:78358469-7835861                             15                          12
## >2:25161598-25161833                             15                          16
##                      >54751950-54752026 468_76BP >78125849-78125923 122_74BP
## >24283548-24283843                            13                          12
## >24283796-24283936                             9                          11
## >7:128241036-1282413                           9                          11
## >7:24283548-24283843                          10                          14
## >25168373-25168611                            15                           9
## >25161598-25161833                            15                          10
## >6:31575210-31575467                           8                          13
## >128241036-128241347                          12                          11
## >78358469-78358619                            10                          12
## >7:24283796-24283936                          10                          10
## >2:25168373-25168611                          12                          12
## >31575210-31575467                            11                           8
## >17:78358469-7835861                          12                          10
## >2:25161598-25161833                          12                           9
##                      >26275973-26276063 226_90BP >6:54751950-54752026 468_76BP
## >24283548-24283843                            10                            10
## >24283796-24283936                            10                            10
## >7:128241036-1282413                          11                             7
## >7:24283548-24283843                          11                             9
## >25168373-25168611                            13                            13
## >25161598-25161833                            13                            13
## >6:31575210-31575467                          12                            13
## >128241036-128241347                          12                            12
## >78358469-78358619                            14                             9
## >7:24283796-24283936                          10                            11
## >2:25168373-25168611                           9                            14
## >31575210-31575467                            10                             9
## >17:78358469-7835861                           8                            14
## >2:25161598-25161833                          10                            12
##                      >12:55273510-55273577 140_67BP
## >24283548-24283843                                6
## >24283796-24283936                               10
## >7:128241036-1282413                             11
## >7:24283548-24283843                             10
## >25168373-25168611                               11
## >25161598-25161833                               12
## >6:31575210-31575467                             13
## >128241036-128241347                             12
## >78358469-78358619                               11
## >7:24283796-24283936                             12
## >2:25168373-25168611                             14
## >31575210-31575467                               11
## >17:78358469-7835861                             12
## >2:25161598-25161833                             14
##                      >4:13436399-13436471 116_72BP >13436399-13436471 116_72BP
## >24283548-24283843                              10                          10
## >24283796-24283936                              11                          12
## >7:128241036-1282413                             9                           8
## >7:24283548-24283843                             9                          11
## >25168373-25168611                              13                          13
## >25161598-25161833                              14                          11
## >6:31575210-31575467                            13                          13
## >128241036-128241347                            12                          14
## >78358469-78358619                              14                          12
## >7:24283796-24283936                            14                          12
## >2:25168373-25168611                            13                          12
## >31575210-31575467                              10                          12
## >17:78358469-7835861                            12                           9
## >2:25161598-25161833                            13                          12
##                      >4:78125849-78125923 122_74BP
## >24283548-24283843                              11
## >24283796-24283936                              11
## >7:128241036-1282413                            11
## >7:24283548-24283843                            12
## >25168373-25168611                              15
## >25161598-25161833                              13
## >6:31575210-31575467                            14
## >128241036-128241347                            14
## >78358469-78358619                              14
## >7:24283796-24283936                            13
## >2:25168373-25168611                            13
## >31575210-31575467                              12
## >17:78358469-7835861                            10
## >2:25161598-25161833                            11
## 
## [[26]]$rowDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 14.28286 
## 
## [[26]]$colDendrogram
## 'dendrogram' with 2 branches and 14 members total, at height 13.92839 
## 
## [[26]]$breaks
##  [1]  6.0  6.2  6.4  6.6  6.8  7.0  7.2  7.4  7.6  7.8  8.0  8.2  8.4  8.6  8.8
## [16]  9.0  9.2  9.4  9.6  9.8 10.0 10.2 10.4 10.6 10.8 11.0 11.2 11.4 11.6 11.8
## [31] 12.0 12.2 12.4 12.6 12.8 13.0 13.2 13.4 13.6 13.8 14.0 14.2 14.4 14.6 14.8
## [46] 15.0 15.2 15.4 15.6 15.8 16.0
## 
## [[26]]$col
##  [1] "#FF0000" "#FF0505" "#FF0A0A" "#FF0F0F" "#FF1414" "#FF1A1A" "#FF1F1F"
##  [8] "#FF2424" "#FF2929" "#FF2E2E" "#FF3434" "#FF3939" "#FF3E3E" "#FF4343"
## [15] "#FF4848" "#FF4E4E" "#FF5353" "#FF5858" "#FF5D5D" "#FF6262" "#FF6868"
## [22] "#FF6D6D" "#FF7272" "#FF7777" "#FF7C7C" "#FF8282" "#FF8787" "#FF8C8C"
## [29] "#FF9191" "#FF9696" "#FF9C9C" "#FFA1A1" "#FFA6A6" "#FFABAB" "#FFB0B0"
## [36] "#FFB6B6" "#FFBBBB" "#FFC0C0" "#FFC5C5" "#FFCACA" "#FFD0D0" "#FFD5D5"
## [43] "#FFDADA" "#FFDFDF" "#FFE4E4" "#FFEAEA" "#FFEFEF" "#FFF4F4" "#FFF9F9"
## [50] "#FFFFFF"
## 
## [[26]]$colorTable
##     low high   color
## 1   6.0  6.2 #FF0000
## 2   6.2  6.4 #FF0505
## 3   6.4  6.6 #FF0A0A
## 4   6.6  6.8 #FF0F0F
## 5   6.8  7.0 #FF1414
## 6   7.0  7.2 #FF1A1A
## 7   7.2  7.4 #FF1F1F
## 8   7.4  7.6 #FF2424
## 9   7.6  7.8 #FF2929
## 10  7.8  8.0 #FF2E2E
## 11  8.0  8.2 #FF3434
## 12  8.2  8.4 #FF3939
## 13  8.4  8.6 #FF3E3E
## 14  8.6  8.8 #FF4343
## 15  8.8  9.0 #FF4848
## 16  9.0  9.2 #FF4E4E
## 17  9.2  9.4 #FF5353
## 18  9.4  9.6 #FF5858
## 19  9.6  9.8 #FF5D5D
## 20  9.8 10.0 #FF6262
## 21 10.0 10.2 #FF6868
## 22 10.2 10.4 #FF6D6D
## 23 10.4 10.6 #FF7272
## 24 10.6 10.8 #FF7777
## 25 10.8 11.0 #FF7C7C
## 26 11.0 11.2 #FF8282
## 27 11.2 11.4 #FF8787
## 28 11.4 11.6 #FF8C8C
## 29 11.6 11.8 #FF9191
## 30 11.8 12.0 #FF9696
## 31 12.0 12.2 #FF9C9C
## 32 12.2 12.4 #FFA1A1
## 33 12.4 12.6 #FFA6A6
## 34 12.6 12.8 #FFABAB
## 35 12.8 13.0 #FFB0B0
## 36 13.0 13.2 #FFB6B6
## 37 13.2 13.4 #FFBBBB
## 38 13.4 13.6 #FFC0C0
## 39 13.6 13.8 #FFC5C5
## 40 13.8 14.0 #FFCACA
## 41 14.0 14.2 #FFD0D0
## 42 14.2 14.4 #FFD5D5
## 43 14.4 14.6 #FFDADA
## 44 14.6 14.8 #FFDFDF
## 45 14.8 15.0 #FFE4E4
## 46 15.0 15.2 #FFEAEA
## 47 15.2 15.4 #FFEFEF
## 48 15.4 15.6 #FFF4F4
## 49 15.6 15.8 #FFF9F9
## 50 15.8 16.0 #FFFFFF
## 
## [[26]]$layout
## [[26]]$layout$lmat
##      [,1] [,2]
## [1,]    4    3
## [2,]    2    1
## 
## [[26]]$layout$lhei
## [1] 1.5 4.0
## 
## [[26]]$layout$lwid
## [1] 1.5 4.0

Look at methylation levels

Looking at the average CpG methylation levels across the whole genome. It shows that total methylation levels are very high across the whole sample set. Pool MM is the unmethylated control with ~20% methylation. Pool M is the methylated control with ~91% methylation.

myfilelist <- list.files("fastq",pattern="vcf_meth_average.tsv", full.names = TRUE)
samplelist <- gsub(".bam.vcf_meth_average.tsv","",myfilelist)

myread2 <- function(myfile){
  read.table(myfile,header=TRUE)
}

z <- lapply(myfilelist, myread2)
zz <- lapply(z,function(x) {tail(x,1)[4] } )
zz <- unlist(zz)
zz <- gsub("%","",zz)
zz <- as.numeric(zz)

nz <- lapply(z,function(x) {tail(x,1)[1] } )
nz <- unname(gsub(".bam","",gsub("fastq/","",unlist(nz))))
names(zz) <- nz

par(mar=c(5, 10, 5, 2))
barplot(zz,horiz=TRUE,las=1,cex.names=0.6,xlab="percent CpG methylation")
grid()

Now I will look at average CpH methylation levels across the whole genome

z <- lapply(myfilelist, myread2)
zz <- lapply(z,function(x) {tail(x,1)[10] } )
zz <- unlist(zz)
zz <- gsub("%","",zz)
zz <- as.numeric(zz)

nz <- lapply(z,function(x) {tail(x,1)[1] } )
nz <- unname(gsub(".bam","",gsub("fastq/","",unlist(nz))))
names(zz) <- nz

par(mar=c(5, 10, 5, 2))
barplot(zz,horiz=TRUE,las=1,cex.names=0.6,xlab="percent CpH methylation")
grid()

cph <- zz

Read in data

myobjf looks strange because if the coverage is high, it gets capped to approx 2623.

file.list <- list.files(DATADIR,pattern="methylkit.tsv",full.names=TRUE)
lines <- lapply(file.list,readLines)
file.list <- file.list[which(lapply(lines,length) > 0)]

samplesheet <- read.table("sample_info/samplesheet_2020-10-15.tsv",sep="\t",header=TRUE)

samplesheet$poolID <- paste("pool",samplesheet$Internal_ID,sep="")

# filter files for those in the sample sheet
file.list <- sapply(strsplit(file.list,"\\."),"[[",1) 

file.list <- sapply(strsplit(file.list,"/"),"[[",2) 

file.list <- file.list[grep("ool",file.list)]
file.list
##  [1] "pool1"  "pool10" "pool11" "pool12" "pool13" "pool14" "pool15" "pool16"
##  [9] "pool17" "pool18" "pool19" "pool2"  "pool20" "pool21" "pool22" "pool23"
## [17] "pool24" "pool3"  "pool4"  "pool5"  "pool6"  "pool7"  "pool8"  "pool9" 
## [25] "PoolM"  "PoolMM"
myobj <- methRead( location=as.list(paste("fastq/",file.list,".methylkit.tsv",sep="")),
  sample.id=as.list(file.list),
  header=FALSE,
  assembly="hg38",
  treatment=sample(1:length(file.list)),
  context="CpG",
  mincov = 0 )
## Received list of locations.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
myobjf <- filterByCoverage(myobj,lo.count=3,lo.perc=NULL,
  hi.count=NULL,hi.perc=NULL)

meth <- unite(myobjf, destrand=FALSE)
## uniting...
percMethylation(meth) %>% kbl() %>% kable_styling()
pool1 pool10 pool11 pool12 pool13 pool14 pool15 pool16 pool17 pool18 pool19 pool2 pool20 pool21 pool22 pool23 pool24 pool3 pool4 pool5 pool6 pool7 pool8 pool9 PoolM PoolMM
44.2105263 51.1055486 51.3513514 35.8905035 58.2954545 60.6260297 62.1198569 49.1853674 44.2940039 60.5173876 68.3053360 57.6923077 58.1673307 52.5090909 66.3100058 53.5913529 61.4853763 66.2091239 64.0079478 60.6912267 52.7004117 52.7762507 64.3000000 42.2116091 95.8333333 2.1739130
70.4086912 70.6868357 61.5835777 72.5033289 68.8107704 68.1793914 67.0198675 60.0120992 54.3859649 68.9970870 72.7094561 69.8062792 70.4879938 64.9988030 71.2933754 67.5954592 69.5133742 72.0015886 74.7972028 73.7020316 61.2987631 62.3767798 72.2986248 50.2881844 95.9016393 1.4492754
80.3860198 71.2183156 74.7093023 80.4045093 78.3996995 78.6133333 81.2914640 68.1928441 70.8938121 80.2083333 79.5104039 75.1087320 80.3937008 77.6044167 78.9863326 78.9872546 79.5110968 85.2824185 88.5913529 90.0037439 79.4908399 75.1776927 79.1133005 56.3898917 99.1869919 2.8169014
34.6013549 29.7107438 31.9526627 29.5949113 35.8848049 28.3776451 32.1828776 27.0064083 29.2083013 35.6991973 35.6045590 35.3872054 24.2687747 34.4067797 40.7087295 35.2039038 34.4995141 32.0064335 40.1075573 39.1089109 30.6004340 30.5908338 34.6898263 30.9044306 100.0000000 1.4285714
71.3006846 69.7809012 65.9763314 49.4952894 71.6082317 71.1938664 71.9116321 61.6000000 63.3966654 75.3202391 76.5931069 63.7159206 71.3375796 67.1068721 73.1104651 68.2121531 75.1973684 71.9902716 79.5953263 71.8904526 60.9000726 56.2015504 73.0150754 53.4926471 99.1525424 3.5971223
66.1949686 61.5833333 65.6716418 50.7075472 72.2919042 69.3144723 75.9209344 60.0983707 57.0987654 70.0000000 76.4078392 69.4989844 61.5873016 64.6915386 71.1967546 70.5159705 73.0111769 75.7009346 79.7968397 72.5928734 65.3036535 64.8783186 76.2024048 52.3178808 96.6942149 3.7037037
52.0207254 45.7084189 45.8579882 52.1056150 59.1960561 58.5831063 59.8839804 44.4920441 35.0115296 55.9966216 59.5907298 49.4963062 48.0252765 46.0962050 50.9962460 47.9064899 49.1039427 59.7008892 55.2957746 50.0944465 44.1056423 44.1176471 56.8159204 40.6102434 99.1452991 0.7352941
91.7808219 95.1515152 88.2352941 94.5454545 98.2608696 91.6666667 96.0526316 96.4285714 97.5903614 95.2941176 95.9595960 96.2962963 84.6153846 93.3333333 95.4248366 97.9591837 92.2705314 90.1408451 96.5517241 93.8271605 95.2380952 97.5000000 98.3333333 92.7710843 95.4773869 66.6666667
98.8925803 99.2296919 100.0000000 98.8313856 99.7117117 98.9552239 99.6784566 99.5786517 99.5953465 99.4958875 99.6054362 99.3464052 98.6168741 99.5045417 99.6022978 99.5934959 99.6946876 99.5092025 99.5783556 99.5927602 99.3131082 99.1243433 99.5711222 99.5898277 99.3984267 85.7142857
85.9266601 90.1098901 93.1034483 93.3232170 85.7844858 84.0852130 92.3591213 91.8953145 91.2904022 95.6923077 99.4152047 72.7649007 95.7158963 74.2062076 95.6972973 94.0958555 90.3996865 89.5991333 95.2114428 96.2914485 97.4884675 92.3437500 92.2701950 89.9062438 99.4871795 88.0000000
78.3143939 72.5853094 85.7142857 80.3183792 81.0986012 85.6796117 79.2088316 80.9072165 81.0999039 85.5014896 70.0934579 72.4778047 86.4097363 68.1959296 83.7009032 84.4049248 74.2009132 82.6844262 85.4277286 88.4183232 84.1841842 83.7349398 79.3758480 68.5073171 86.0016420 79.4117647
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1.5969030 2.6873581 1.0498688 2.9050279 2.5000000 2.0909393 2.3096355 1.8939394 3.0120482 1.9138756 1.4885310 1.8933272 1.9241653 2.5065696 2.3902741 1.3991163 2.2139071 3.0079804 3.9091505 2.9116466 2.7080344 2.2046159 1.4127424 1.4939916 96.8955786 0.0884173
15.8536585 23.6024845 8.6956522 24.2574257 17.6100629 20.4545455 36.0360360 11.1627907 20.5741627 14.2361111 24.7093023 11.9658120 21.6374269 20.6060606 24.8756219 10.3896104 4.1666667 25.0000000 10.4895105 13.8888889 23.4939759 8.4337349 26.5822785 16.0427807 100.0000000 5.4545455
26.8292683 12.3456790 4.3478261 24.0000000 29.6296296 19.5652174 27.8260870 15.2073733 12.6760563 11.6838488 10.5882353 7.5630252 12.5000000 19.7604790 18.8775510 19.2307692 22.2222222 19.4805195 16.6666667 16.3636364 9.6969697 12.1951220 21.2500000 17.0329670 99.7126437 5.3892216
15.4761905 19.5121951 29.1666667 27.8606965 30.4878049 6.6666667 28.0701754 14.6118721 15.7407407 16.4383562 21.7008798 11.9658120 15.6976744 12.5748503 20.6030151 14.1025641 21.2765957 23.7500000 9.8591549 15.0943396 13.4146341 8.3333333 22.0779221 11.4130435 100.0000000 5.2941176
20.0000000 19.8795181 4.3478261 17.7339901 27.4390244 11.7021277 25.0000000 10.7623318 17.3708920 8.0808081 15.1428571 7.6923077 14.5251397 13.5294118 22.1674877 15.1898734 18.0000000 12.9870130 18.0555556 8.2568807 12.7906977 4.7058824 7.5000000 10.1063830 100.0000000 5.2941176
17.8571429 11.8012422 0.0000000 4.0000000 17.6100629 10.1123596 20.3539823 7.4766355 14.0776699 11.3013699 11.6279070 9.2436975 12.0000000 8.2840237 22.4489796 11.5384615 8.0000000 16.4556962 12.4087591 9.5238095 12.5748503 7.1428571 14.6666667 3.2258065 100.0000000 5.3254438
34.9397590 12.5786164 0.0000000 30.0492611 13.0434783 16.3043478 24.5614035 10.8490566 11.0047847 9.8245614 15.7270030 6.7796610 13.9534884 12.5748503 25.0000000 17.9487179 14.8936170 16.0000000 13.1944444 5.5045872 12.5748503 12.1951220 7.4074074 4.9723757 100.0000000 5.3254438
17.3469388 5.4545455 12.0000000 5.7268722 14.1304348 4.7169811 11.6788321 10.0775194 8.5365854 8.1005587 6.0532688 4.4776119 3.5532995 3.5714286 14.2857143 6.1111111 6.7796610 5.3763441 6.1797753 4.8000000 6.5000000 5.8823529 3.0303030 2.2935780 100.0000000 4.7337278
28.7128713 20.9580838 7.1428571 8.1784387 16.5919283 7.9365079 34.0277778 8.5324232 11.9133574 11.2531969 13.8828633 12.1951220 7.7868852 10.9649123 26.5625000 8.3333333 4.1095890 12.6213592 9.6256684 12.8378378 8.8235294 17.2413793 13.9130435 11.4173228 99.7150997 5.2631579
9.7402597 16.1676647 2.2727273 8.8471850 8.5245902 5.1724138 14.7058824 4.9763033 2.9197080 4.1218638 8.5803432 3.4334764 7.3619632 7.0063694 12.6760563 5.7627119 8.7912088 6.8027211 2.8070175 3.2710280 8.2018927 3.7267081 3.8216561 5.7471264 100.0000000 5.2631579
2.9761905 13.5802469 7.1428571 15.2112676 8.0906149 7.5144509 15.6565657 4.9411765 5.2896725 5.3406998 3.2448378 4.4052863 5.0147493 5.5384615 10.5555556 7.8231293 0.0000000 5.1948052 6.7137809 11.3861386 4.2424242 1.8072289 6.4102564 9.0909091 100.0000000 5.9171598
10.2564103 4.7619048 2.5641026 15.0417827 6.7340067 2.3668639 10.1941748 6.5000000 7.6315789 4.6554935 2.6813880 3.1390135 3.6923077 1.6129032 8.7570621 4.3478261 4.5454545 5.7142857 9.0225564 4.8780488 2.5889968 0.0000000 6.4102564 3.1976744 84.4311377 5.8139535
7.6433121 10.6508876 0.0000000 19.3732194 8.6092715 10.7784431 14.7058824 5.1851852 4.8387097 5.8270677 3.1152648 6.4516129 4.3478261 4.3189369 5.5096419 9.3525180 5.7471264 3.4722222 5.3435115 6.4676617 4.9079755 3.1847134 12.9032258 3.9436620 100.0000000 5.2325581
2.4096386 6.4705882 2.1739130 15.8038147 2.1406728 0.0000000 8.2949309 3.9080460 3.1707317 5.3191489 1.4684288 1.6528926 2.5936599 1.8292683 5.9740260 7.3825503 2.0833333 1.2578616 2.0979021 1.8518519 3.2258065 1.1976048 3.0864198 0.2638522 100.0000000 5.1724138
7.8125000 9.5808383 0.0000000 20.1438849 5.4166667 4.8611111 13.0434783 7.1823204 7.0063694 4.7227926 5.5956679 5.2910053 5.1181102 6.9230769 8.0267559 5.0209205 1.2048193 2.5000000 7.2033898 4.9689441 4.1237113 6.9767442 17.8294574 8.1560284 100.0000000 7.6023392
13.1736527 11.5151515 2.2222222 0.0000000 18.6119874 3.2608696 27.8761062 16.5532880 7.5829384 11.0356537 14.3063584 14.7540984 9.1954023 10.2719033 18.5000000 20.0636943 0.0000000 12.9870130 14.3835616 11.1111111 11.1764706 7.6470588 13.1736527 8.7671233 99.7289973 5.8479532
14.2011834 5.9880240 8.8888889 9.8522167 10.8433735 4.2780749 11.6883117 11.0859729 8.2547170 3.5593220 3.8406828 5.2845528 3.1428571 3.8690476 4.0000000 13.2492114 8.0000000 8.9171975 7.1186441 5.3811659 8.7976540 2.9069767 5.3254438 5.8981233 99.4520548 5.2023121
9.5238095 5.3892216 0.0000000 0.0000000 10.5919003 1.0928962 15.9817352 3.0023095 7.2639225 6.0658579 5.1020408 4.6413502 0.0000000 4.2682927 8.3969466 3.1645570 9.4736842 5.0955414 0.6779661 6.0747664 2.6548673 4.7619048 7.7844311 4.6575342 100.0000000 5.8479532
14.1975309 15.6626506 8.6956522 16.4102564 7.1651090 2.2222222 22.5225225 2.5761124 7.1065990 3.8869258 5.3097345 8.5106383 2.6162791 12.6934985 13.0319149 10.0649351 4.1237113 9.0322581 2.7972028 4.8076923 2.4242424 3.6585366 4.7058824 3.3149171 70.7520891 6.4327485
13.2947977 10.2409639 0.0000000 3.8929440 7.3846154 1.0928962 20.8888889 0.6741573 4.9528302 8.7030717 3.1700288 5.3497942 3.9548023 9.0634441 14.6529563 7.0063694 0.0000000 7.5000000 9.9315068 8.2191781 2.9325513 1.1764706 5.8479532 6.1662198 71.1911357 4.7619048
10.9090909 12.7272727 4.3478261 14.7959184 11.3496933 9.3922652 22.6244344 4.8387097 9.7087379 6.8493151 3.3773862 7.6595745 5.5072464 5.7228916 7.3232323 3.8585209 13.1313131 9.6153846 13.3561644 10.0456621 4.6783626 3.5502959 4.1666667 9.2643052 87.9888268 5.9171598
33.5443038 35.5828221 13.9534884 29.6587927 42.3076923 30.4597701 67.3076923 41.0138249 33.3333333 34.3580470 32.0726172 33.3333333 25.7763975 31.4465409 34.5108696 25.7425743 42.1052632 26.7973856 32.1299639 29.8507463 39.5705521 27.5000000 32.7044025 36.0563380 99.1825613 4.7058824
15.1515152 20.1298701 4.3478261 6.8354430 13.7931034 5.5555556 29.7777778 8.7155963 12.4688279 13.3099825 10.1321586 13.0252101 8.9552239 16.6144201 11.8421053 14.0065147 8.9887640 17.6470588 11.3793103 16.0377358 8.4592145 4.8780488 6.7484663 13.1868132 62.8834356 3.0303030
29.3750000 23.4177215 9.0909091 37.9032258 17.9738562 7.5144509 31.9634703 10.0719424 21.6931217 15.5303030 19.7530864 17.5438596 14.2857143 11.8210863 24.8677249 12.5412541 11.6279070 16.8831169 19.5488722 15.1960784 9.8726115 11.9205298 17.5324675 22.7528090 99.4475138 4.7904192
34.6666667 42.8571429 22.7272727 50.9536785 25.2595156 21.6867470 49.0384615 27.9301746 25.9259259 29.0944123 26.9789984 26.9406393 27.9069767 42.3487544 32.0113314 28.0701754 19.3181818 20.6896552 29.6296296 15.0753769 26.5175719 23.3333333 38.1944444 33.4337349 99.6774194 0.7692308
13.0952381 15.9763314 6.8181818 23.3082707 12.6934985 8.1081081 17.1806167 12.8146453 17.4876847 14.3589744 8.1991215 14.9377593 13.5211268 8.7087087 13.9650873 12.0634921 3.1578947 6.2893082 16.7808219 4.5662100 8.5798817 14.3712575 5.4878049 7.3170732 99.7267760 4.1916168
14.2857143 16.9230769 27.7777778 26.6666667 19.8630137 9.5890411 20.4301075 21.9251337 19.2982456 13.3064516 15.9169550 15.5339806 29.6052632 14.0625000 17.9012346 11.9402985 11.6279070 8.5714286 17.5000000 5.9523810 8.6666667 14.0845070 23.9436620 12.0253165 99.7067449 5.9259259
12.3456790 20.7792208 18.1818182 35.3846154 18.1250000 10.0000000 33.6363636 23.9234450 21.7391304 16.7259786 29.2035398 20.8333333 23.2558140 24.5398773 27.1794872 18.1818182 31.9148936 20.7792208 21.8309859 20.1923077 10.1190476 8.7500000 14.8148148 10.4972376 68.2719547 5.5214724
45.5696203 44.8051948 61.9047619 65.9459459 40.9090909 33.3333333 54.1284404 40.1913876 43.6170213 53.2374101 33.0330330 45.5357143 40.6976744 33.3333333 37.7659574 37.5838926 23.9130435 30.6666667 30.9352518 39.8058252 46.8750000 43.5897436 43.0379747 32.9608939 100.0000000 5.0000000
44.9275362 39.5683453 15.0000000 46.2857143 33.3333333 28.3950617 58.8785047 40.7216495 47.9289941 41.8326693 37.0129870 35.1851852 24.6666667 39.8550725 44.8863636 33.5820896 23.2558140 34.7826087 34.1269841 28.7234043 37.7622378 28.5714286 51.3157895 23.7804878 100.0000000 6.3380282
57.5342466 48.9795918 45.0000000 51.7045455 45.2702703 38.1578947 59.0476190 38.5000000 50.0000000 52.4904215 44.6308725 45.7142857 34.7826087 45.2054795 50.5681818 34.2857143 41.0256410 43.9393939 38.8059701 40.6250000 42.1052632 36.7647059 40.2777778 42.7710843 100.0000000 5.8394161

Export data for downstream analysis

Here I’m exporting the number of Cs and Ts at each position. Then I’m also providing the beta values.

mytable <- getData(meth)

write.table(x=mytable,file="methylation_data.tsv",sep="\t",quote=FALSE,row.names=FALSE)

mytable2 <- percMethylation(meth)

mytable3 <- cbind(mytable[,1:3],mytable2)

write.table(x=mytable3,file="methylation_betavals.tsv",sep="\t",quote=FALSE,row.names=FALSE)

Proportion of CpG sites with usable data

  • Percent CpG sites with usable data
fa <- read.fasta("amplicons_hg38.bed.fa")

# count CpG sites
cnt_cpg <- function(fa1) {
  length(which(
    sapply( 1:(length(fa1)-1), function(i) {
      motif <- fa1[i:(i+1)]
      sum(as.numeric(motif == c("c","g")) )==2  
    })
  ))
}

num_cpg <- lapply(fa, cnt_cpg)

start_pos <- sapply(strsplit(names(num_cpg),":"),"[[",2)
start_pos <- sapply(strsplit(start_pos,"-"),"[[",1)

end_pos <- sapply(strsplit(names(num_cpg),":"),"[[",2)
end_pos <- sapply(strsplit(end_pos,"-"),"[[",2)

chrs <- sapply(strsplit(names(num_cpg),":"),"[[",1)

res <- lapply(1:length(num_cpg),function(i) {
  mychr <- chrs[i]
  mysubset <- mytable3[ which(mytable3$chr==mychr),]
  mystart <- start_pos[i]
  mysubset <- mysubset[which(mysubset$start > mystart),]
  myend <- end_pos[i]
  mysubset <- mysubset[which(mysubset$end < myend),]
  nrow(mysubset)
})

mydf <- as.data.frame(unlist(num_cpg))

mydf$covered_cpg <- unlist(res)

colnames(mydf)[1] <- "num_CpGs"

mydf %>% kbl() %>% kable_styling()
num_CpGs covered_cpg
17:78358469-78358619 7 7
2:25161598-25161833 26 26
2:25168373-25168611 28 0
6:31575210-31575467 8 8
7:24283548-24283843 16 16
7:24283796-24283936 5 5
7:128241036-128241347 31 30

Basic plots

getCorrelation(meth,plot=TRUE)
##            pool1    pool10    pool11    pool12    pool13    pool14    pool15
## pool1  1.0000000 0.9686140 0.9646152 0.9671968 0.9800029 0.9844748 0.9809130
## pool10 0.9686140 1.0000000 0.9677930 0.9542965 0.9574251 0.9766997 0.9469722
## pool11 0.9646152 0.9677930 1.0000000 0.9599687 0.9562122 0.9681229 0.9409967
## pool12 0.9671968 0.9542965 0.9599687 1.0000000 0.9560373 0.9582407 0.9555830
## pool13 0.9800029 0.9574251 0.9562122 0.9560373 1.0000000 0.9766965 0.9769442
## pool14 0.9844748 0.9766997 0.9681229 0.9582407 0.9766965 1.0000000 0.9656264
## pool15 0.9809130 0.9469722 0.9409967 0.9555830 0.9769442 0.9656264 1.0000000
## pool16 0.9804794 0.9841877 0.9740267 0.9580132 0.9728363 0.9837550 0.9648048
## pool17 0.9843373 0.9770348 0.9736619 0.9637101 0.9710616 0.9829231 0.9680020
## pool18 0.9883871 0.9720777 0.9707586 0.9637344 0.9822067 0.9863576 0.9791588
## pool19 0.9833118 0.9689121 0.9601395 0.9564762 0.9825724 0.9844575 0.9774845
## pool2  0.9793783 0.9712971 0.9685827 0.9635627 0.9764209 0.9810620 0.9699718
## pool20 0.9847569 0.9753736 0.9757521 0.9645586 0.9772279 0.9892249 0.9705783
## pool21 0.9815487 0.9797288 0.9669327 0.9685774 0.9719447 0.9856450 0.9691192
## pool22 0.9899928 0.9654667 0.9596614 0.9570439 0.9842715 0.9840352 0.9840538
## pool23 0.9762508 0.9710549 0.9638446 0.9571882 0.9740411 0.9815250 0.9576326
## pool24 0.9826875 0.9708395 0.9727604 0.9570780 0.9790940 0.9881717 0.9676369
## pool3  0.9811607 0.9691977 0.9612452 0.9552345 0.9824457 0.9863586 0.9723400
## pool4  0.9820189 0.9650579 0.9619726 0.9495763 0.9816079 0.9832560 0.9714213
## pool5  0.9831481 0.9714966 0.9694796 0.9545339 0.9790436 0.9868997 0.9714101
## pool6  0.9890178 0.9760349 0.9746538 0.9653127 0.9796316 0.9893479 0.9769611
## pool7  0.9796586 0.9723353 0.9663075 0.9586774 0.9805615 0.9837378 0.9593856
## pool8  0.9823621 0.9681906 0.9653899 0.9614847 0.9805934 0.9833393 0.9768064
## pool9  0.9822698 0.9774732 0.9740198 0.9648510 0.9708775 0.9822815 0.9661920
## PoolM  0.1830119 0.1822520 0.1627453 0.1955849 0.2431440 0.1689727 0.1864937
## PoolMM 0.8391721 0.8300280 0.8114536 0.8224105 0.8595989 0.8316251 0.8197087
##           pool16    pool17    pool18    pool19     pool2    pool20    pool21
## pool1  0.9804794 0.9843373 0.9883871 0.9833118 0.9793783 0.9847569 0.9815487
## pool10 0.9841877 0.9770348 0.9720777 0.9689121 0.9712971 0.9753736 0.9797288
## pool11 0.9740267 0.9736619 0.9707586 0.9601395 0.9685827 0.9757521 0.9669327
## pool12 0.9580132 0.9637101 0.9637344 0.9564762 0.9635627 0.9645586 0.9685774
## pool13 0.9728363 0.9710616 0.9822067 0.9825724 0.9764209 0.9772279 0.9719447
## pool14 0.9837550 0.9829231 0.9863576 0.9844575 0.9810620 0.9892249 0.9856450
## pool15 0.9648048 0.9680020 0.9791588 0.9774845 0.9699718 0.9705783 0.9691192
## pool16 1.0000000 0.9889649 0.9829374 0.9802303 0.9765107 0.9884553 0.9799709
## pool17 0.9889649 1.0000000 0.9846336 0.9754046 0.9745931 0.9883807 0.9805916
## pool18 0.9829374 0.9846336 1.0000000 0.9874680 0.9867965 0.9881144 0.9844406
## pool19 0.9802303 0.9754046 0.9874680 1.0000000 0.9867825 0.9866028 0.9830568
## pool2  0.9765107 0.9745931 0.9867965 0.9867825 1.0000000 0.9789463 0.9909652
## pool20 0.9884553 0.9883807 0.9881144 0.9866028 0.9789463 1.0000000 0.9816768
## pool21 0.9799709 0.9805916 0.9844406 0.9830568 0.9909652 0.9816768 1.0000000
## pool22 0.9810569 0.9840853 0.9891590 0.9886140 0.9773654 0.9886484 0.9783771
## pool23 0.9756081 0.9765019 0.9782272 0.9751134 0.9749364 0.9801330 0.9808282
## pool24 0.9832069 0.9821842 0.9838654 0.9859697 0.9825797 0.9868053 0.9843022
## pool3  0.9758655 0.9722346 0.9870965 0.9907363 0.9841706 0.9827739 0.9822831
## pool4  0.9824283 0.9805524 0.9835064 0.9844367 0.9727931 0.9884899 0.9721813
## pool5  0.9839485 0.9847904 0.9859786 0.9845782 0.9754142 0.9912610 0.9771664
## pool6  0.9890101 0.9918424 0.9911925 0.9866737 0.9851592 0.9912416 0.9857091
## pool7  0.9830570 0.9811826 0.9782986 0.9762426 0.9743060 0.9812904 0.9771809
## pool8  0.9787919 0.9770918 0.9895079 0.9893905 0.9891796 0.9828959 0.9866343
## pool9  0.9846963 0.9864884 0.9835734 0.9758289 0.9801890 0.9823853 0.9863912
## PoolM  0.1784083 0.1751420 0.1665435 0.1705830 0.1557932 0.1703691 0.1541538
## PoolMM 0.8603311 0.8503065 0.8312309 0.8298285 0.8136014 0.8465418 0.8156806
##           pool22    pool23    pool24     pool3     pool4     pool5     pool6
## pool1  0.9899928 0.9762508 0.9826875 0.9811607 0.9820189 0.9831481 0.9890178
## pool10 0.9654667 0.9710549 0.9708395 0.9691977 0.9650579 0.9714966 0.9760349
## pool11 0.9596614 0.9638446 0.9727604 0.9612452 0.9619726 0.9694796 0.9746538
## pool12 0.9570439 0.9571882 0.9570780 0.9552345 0.9495763 0.9545339 0.9653127
## pool13 0.9842715 0.9740411 0.9790940 0.9824457 0.9816079 0.9790436 0.9796316
## pool14 0.9840352 0.9815250 0.9881717 0.9863586 0.9832560 0.9868997 0.9893479
## pool15 0.9840538 0.9576326 0.9676369 0.9723400 0.9714213 0.9714101 0.9769611
## pool16 0.9810569 0.9756081 0.9832069 0.9758655 0.9824283 0.9839485 0.9890101
## pool17 0.9840853 0.9765019 0.9821842 0.9722346 0.9805524 0.9847904 0.9918424
## pool18 0.9891590 0.9782272 0.9838654 0.9870965 0.9835064 0.9859786 0.9911925
## pool19 0.9886140 0.9751134 0.9859697 0.9907363 0.9844367 0.9845782 0.9866737
## pool2  0.9773654 0.9749364 0.9825797 0.9841706 0.9727931 0.9754142 0.9851592
## pool20 0.9886484 0.9801330 0.9868053 0.9827739 0.9884899 0.9912610 0.9912416
## pool21 0.9783771 0.9808282 0.9843022 0.9822831 0.9721813 0.9771664 0.9857091
## pool22 1.0000000 0.9747681 0.9834141 0.9830170 0.9903463 0.9884849 0.9901106
## pool23 0.9747681 1.0000000 0.9797276 0.9746924 0.9711361 0.9794025 0.9827784
## pool24 0.9834141 0.9797276 1.0000000 0.9817057 0.9825255 0.9858075 0.9891570
## pool3  0.9830170 0.9746924 0.9817057 1.0000000 0.9789947 0.9814283 0.9823688
## pool4  0.9903463 0.9711361 0.9825255 0.9789947 1.0000000 0.9932338 0.9850831
## pool5  0.9884849 0.9794025 0.9858075 0.9814283 0.9932338 1.0000000 0.9894326
## pool6  0.9901106 0.9827784 0.9891570 0.9823688 0.9850831 0.9894326 1.0000000
## pool7  0.9786787 0.9883015 0.9799857 0.9723199 0.9776920 0.9823807 0.9863953
## pool8  0.9848245 0.9741928 0.9822549 0.9867609 0.9802695 0.9795862 0.9870350
## pool9  0.9755593 0.9778436 0.9812686 0.9760814 0.9683549 0.9749323 0.9868380
## PoolM  0.1884014 0.2095912 0.1594451 0.1678360 0.1839793 0.1710796 0.1685785
## PoolMM 0.8500221 0.8278538 0.8221364 0.8315431 0.8472041 0.8427918 0.8443198
##            pool7     pool8     pool9     PoolM    PoolMM
## pool1  0.9796586 0.9823621 0.9822698 0.1830119 0.8391721
## pool10 0.9723353 0.9681906 0.9774732 0.1822520 0.8300280
## pool11 0.9663075 0.9653899 0.9740198 0.1627453 0.8114536
## pool12 0.9586774 0.9614847 0.9648510 0.1955849 0.8224105
## pool13 0.9805615 0.9805934 0.9708775 0.2431440 0.8595989
## pool14 0.9837378 0.9833393 0.9822815 0.1689727 0.8316251
## pool15 0.9593856 0.9768064 0.9661920 0.1864937 0.8197087
## pool16 0.9830570 0.9787919 0.9846963 0.1784083 0.8603311
## pool17 0.9811826 0.9770918 0.9864884 0.1751420 0.8503065
## pool18 0.9782986 0.9895079 0.9835734 0.1665435 0.8312309
## pool19 0.9762426 0.9893905 0.9758289 0.1705830 0.8298285
## pool2  0.9743060 0.9891796 0.9801890 0.1557932 0.8136014
## pool20 0.9812904 0.9828959 0.9823853 0.1703691 0.8465418
## pool21 0.9771809 0.9866343 0.9863912 0.1541538 0.8156806
## pool22 0.9786787 0.9848245 0.9755593 0.1884014 0.8500221
## pool23 0.9883015 0.9741928 0.9778436 0.2095912 0.8278538
## pool24 0.9799857 0.9822549 0.9812686 0.1594451 0.8221364
## pool3  0.9723199 0.9867609 0.9760814 0.1678360 0.8315431
## pool4  0.9776920 0.9802695 0.9683549 0.1839793 0.8472041
## pool5  0.9823807 0.9795862 0.9749323 0.1710796 0.8427918
## pool6  0.9863953 0.9870350 0.9868380 0.1685785 0.8443198
## pool7  1.0000000 0.9739478 0.9793116 0.2275080 0.8570260
## pool8  0.9739478 1.0000000 0.9771235 0.1767719 0.8201381
## pool9  0.9793116 0.9771235 1.0000000 0.1645937 0.8476075
## PoolM  0.2275080 0.1767719 0.1645937 1.0000000 0.2204892
## PoolMM 0.8570260 0.8201381 0.8476075 0.2204892 1.0000000

clusterSamples(meth, dist="correlation", method="ward", plot=TRUE)
## The "ward" method has been renamed to "ward.D"; note new "ward.D2"

## 
## Call:
## hclust(d = d, method = HCLUST.METHODS[hclust.method])
## 
## Cluster method   : ward.D 
## Distance         : pearson 
## Number of objects: 26
PCASamples(meth, screeplot=TRUE)

pc <- PCASamples(meth,obj.return=TRUE)

plot(pc$x[,1],pc$x[,2],bty="n",type="n")
grid()
text(pc$x[,1],pc$x[,2],labels=rownames(pc$x),cex=0.7)

Now to remove control samples and others not included on the samplesheet.

file.list <- file.list[which(file.list %in% samplesheet$poolID)]

# filter samplesheet for those with files
samplesheet <- samplesheet[which( samplesheet$poolID  %in% file.list ),]

myobj <- methRead( location=as.list(paste("fastq/",file.list,".methylkit.tsv",sep="")),
  sample.id=as.list(samplesheet$poolID),
  header=FALSE,
  assembly="hg38",
  treatment=samplesheet$GWG,
  context="CpG",
  mincov = 5 )
## Received list of locations.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
myobjf <- filterByCoverage(myobj,lo.count=5,lo.perc=NULL,
  hi.count=NULL,hi.perc=NULL)

meth <- unite(myobjf, destrand=FALSE)
## uniting...
# run another PCA analysis
getCorrelation(meth,plot=TRUE)
##            pool5    pool11    pool12    pool18    pool20    pool19     pool9
## pool5  1.0000000 0.9563093 0.9680151 0.9666401 0.9777120 0.9808063 0.9815729
## pool11 0.9563093 1.0000000 0.9535432 0.9376896 0.9405706 0.9572034 0.9359194
## pool12 0.9680151 0.9535432 1.0000000 0.9604026 0.9573077 0.9693893 0.9465748
## pool18 0.9666401 0.9376896 0.9604026 1.0000000 0.9622638 0.9631222 0.9549016
## pool20 0.9777120 0.9405706 0.9573077 0.9622638 1.0000000 0.9781469 0.9709876
## pool19 0.9808063 0.9572034 0.9693893 0.9631222 0.9781469 1.0000000 0.9634665
## pool9  0.9815729 0.9359194 0.9465748 0.9549016 0.9709876 0.9634665 1.0000000
## pool14 0.9780852 0.9634994 0.9741977 0.9634422 0.9763934 0.9856434 0.9618341
## pool16 0.9785444 0.9555693 0.9688982 0.9660912 0.9713283 0.9811943 0.9624942
## pool7  0.9895428 0.9556948 0.9735333 0.9611447 0.9770532 0.9809402 0.9799526
## pool10 0.9801700 0.9503693 0.9619082 0.9622695 0.9826172 0.9858435 0.9752330
## pool15 0.9754716 0.9484289 0.9671262 0.9685426 0.9796823 0.9820061 0.9646626
## pool6  0.9826724 0.9542636 0.9752599 0.9687567 0.9791817 0.9892856 0.9685015
## pool4  0.9790812 0.9590931 0.9680522 0.9721872 0.9756817 0.9872483 0.9654603
## pool13 0.9862903 0.9499909 0.9628320 0.9610674 0.9833462 0.9860572 0.9799956
## pool21 0.9758085 0.9537123 0.9653966 0.9628359 0.9774859 0.9831502 0.9570905
## pool22 0.9796600 0.9507727 0.9722183 0.9627875 0.9800279 0.9886083 0.9664387
## pool3  0.9787289 0.9499941 0.9616626 0.9617469 0.9848133 0.9868297 0.9678320
## pool23 0.9757320 0.9437029 0.9569218 0.9301664 0.9585953 0.9604974 0.9648743
## pool1  0.9839242 0.9589371 0.9732010 0.9530147 0.9744686 0.9828701 0.9719953
## pool2  0.9894509 0.9610423 0.9774602 0.9629079 0.9755070 0.9850180 0.9772413
## pool24 0.9767175 0.9512030 0.9663656 0.9641719 0.9818018 0.9846547 0.9578525
## pool8  0.9762158 0.9453353 0.9629491 0.9649161 0.9783438 0.9821816 0.9737239
## pool17 0.9797466 0.9564654 0.9734002 0.9691014 0.9739639 0.9841485 0.9637067
##           pool14    pool16     pool7    pool10    pool15     pool6     pool4
## pool5  0.9780852 0.9785444 0.9895428 0.9801700 0.9754716 0.9826724 0.9790812
## pool11 0.9634994 0.9555693 0.9556948 0.9503693 0.9484289 0.9542636 0.9590931
## pool12 0.9741977 0.9688982 0.9735333 0.9619082 0.9671262 0.9752599 0.9680522
## pool18 0.9634422 0.9660912 0.9611447 0.9622695 0.9685426 0.9687567 0.9721872
## pool20 0.9763934 0.9713283 0.9770532 0.9826172 0.9796823 0.9791817 0.9756817
## pool19 0.9856434 0.9811943 0.9809402 0.9858435 0.9820061 0.9892856 0.9872483
## pool9  0.9618341 0.9624942 0.9799526 0.9752330 0.9646626 0.9685015 0.9654603
## pool14 1.0000000 0.9864699 0.9783652 0.9815199 0.9790506 0.9892715 0.9831794
## pool16 0.9864699 1.0000000 0.9761949 0.9742933 0.9728811 0.9866470 0.9794969
## pool7  0.9783652 0.9761949 1.0000000 0.9820409 0.9795117 0.9837336 0.9797803
## pool10 0.9815199 0.9742933 0.9820409 1.0000000 0.9871630 0.9866162 0.9837466
## pool15 0.9790506 0.9728811 0.9795117 0.9871630 1.0000000 0.9799285 0.9909937
## pool6  0.9892715 0.9866470 0.9837336 0.9866162 0.9799285 1.0000000 0.9838958
## pool4  0.9831794 0.9794969 0.9797803 0.9837466 0.9909937 0.9838958 1.0000000
## pool13 0.9830067 0.9814727 0.9843269 0.9885072 0.9772241 0.9889008 0.9808297
## pool21 0.9789707 0.9764804 0.9753710 0.9768158 0.9772377 0.9829280 0.9835878
## pool22 0.9841587 0.9824705 0.9788892 0.9873259 0.9833265 0.9874562 0.9849885
## pool3  0.9790901 0.9731390 0.9812515 0.9901737 0.9857433 0.9849445 0.9846880
## pool23 0.9604109 0.9542158 0.9798271 0.9613928 0.9484319 0.9663471 0.9517296
## pool1  0.9803822 0.9762697 0.9869247 0.9798420 0.9699832 0.9859932 0.9745331
## pool2  0.9846424 0.9835938 0.9917928 0.9819529 0.9786056 0.9863012 0.9817114
## pool24 0.9844542 0.9792174 0.9737323 0.9788961 0.9767644 0.9826205 0.9794268
## pool8  0.9773168 0.9740394 0.9802743 0.9894376 0.9872883 0.9815502 0.9837951
## pool17 0.9863794 0.9847159 0.9789428 0.9780222 0.9814210 0.9849176 0.9881471
##           pool13    pool21    pool22     pool3    pool23     pool1     pool2
## pool5  0.9862903 0.9758085 0.9796600 0.9787289 0.9757320 0.9839242 0.9894509
## pool11 0.9499909 0.9537123 0.9507727 0.9499941 0.9437029 0.9589371 0.9610423
## pool12 0.9628320 0.9653966 0.9722183 0.9616626 0.9569218 0.9732010 0.9774602
## pool18 0.9610674 0.9628359 0.9627875 0.9617469 0.9301664 0.9530147 0.9629079
## pool20 0.9833462 0.9774859 0.9800279 0.9848133 0.9585953 0.9744686 0.9755070
## pool19 0.9860572 0.9831502 0.9886083 0.9868297 0.9604974 0.9828701 0.9850180
## pool9  0.9799956 0.9570905 0.9664387 0.9678320 0.9648743 0.9719953 0.9772413
## pool14 0.9830067 0.9789707 0.9841587 0.9790901 0.9604109 0.9803822 0.9846424
## pool16 0.9814727 0.9764804 0.9824705 0.9731390 0.9542158 0.9762697 0.9835938
## pool7  0.9843269 0.9753710 0.9788892 0.9812515 0.9798271 0.9869247 0.9917928
## pool10 0.9885072 0.9768158 0.9873259 0.9901737 0.9613928 0.9798420 0.9819529
## pool15 0.9772241 0.9772377 0.9833265 0.9857433 0.9484319 0.9699832 0.9786056
## pool6  0.9889008 0.9829280 0.9874562 0.9849445 0.9663471 0.9859932 0.9863012
## pool4  0.9808297 0.9835878 0.9849885 0.9846880 0.9517296 0.9745331 0.9817114
## pool13 1.0000000 0.9772053 0.9837275 0.9834984 0.9689537 0.9853962 0.9863770
## pool21 0.9772053 1.0000000 0.9812058 0.9784270 0.9521473 0.9764912 0.9796255
## pool22 0.9837275 0.9812058 1.0000000 0.9828888 0.9597880 0.9805891 0.9840617
## pool3  0.9834984 0.9784270 0.9828888 1.0000000 0.9552981 0.9762199 0.9774207
## pool23 0.9689537 0.9521473 0.9597880 0.9552981 1.0000000 0.9871625 0.9801812
## pool1  0.9853962 0.9764912 0.9805891 0.9762199 0.9871625 1.0000000 0.9905862
## pool2  0.9863770 0.9796255 0.9840617 0.9774207 0.9801812 0.9905862 1.0000000
## pool24 0.9797280 0.9884524 0.9815826 0.9753317 0.9546272 0.9772414 0.9810819
## pool8  0.9819853 0.9738501 0.9833155 0.9843079 0.9529379 0.9712346 0.9781993
## pool17 0.9784799 0.9808928 0.9826017 0.9796756 0.9473584 0.9716792 0.9819112
##           pool24     pool8    pool17
## pool5  0.9767175 0.9762158 0.9797466
## pool11 0.9512030 0.9453353 0.9564654
## pool12 0.9663656 0.9629491 0.9734002
## pool18 0.9641719 0.9649161 0.9691014
## pool20 0.9818018 0.9783438 0.9739639
## pool19 0.9846547 0.9821816 0.9841485
## pool9  0.9578525 0.9737239 0.9637067
## pool14 0.9844542 0.9773168 0.9863794
## pool16 0.9792174 0.9740394 0.9847159
## pool7  0.9737323 0.9802743 0.9789428
## pool10 0.9788961 0.9894376 0.9780222
## pool15 0.9767644 0.9872883 0.9814210
## pool6  0.9826205 0.9815502 0.9849176
## pool4  0.9794268 0.9837951 0.9881471
## pool13 0.9797280 0.9819853 0.9784799
## pool21 0.9884524 0.9738501 0.9808928
## pool22 0.9815826 0.9833155 0.9826017
## pool3  0.9753317 0.9843079 0.9796756
## pool23 0.9546272 0.9529379 0.9473584
## pool1  0.9772414 0.9712346 0.9716792
## pool2  0.9810819 0.9781993 0.9819112
## pool24 1.0000000 0.9747160 0.9811697
## pool8  0.9747160 1.0000000 0.9764140
## pool17 0.9811697 0.9764140 1.0000000

clusterSamples(meth, dist="correlation", method="ward", plot=TRUE)
## The "ward" method has been renamed to "ward.D"; note new "ward.D2"

## 
## Call:
## hclust(d = d, method = HCLUST.METHODS[hclust.method])
## 
## Cluster method   : ward.D 
## Distance         : pearson 
## Number of objects: 24
PCASamples(meth, screeplot=TRUE)

pc <- PCASamples(meth,obj.return=TRUE)

plot(pc$x[,1],pc$x[,2],bty="n",type="n")
grid()
text(pc$x[,1],pc$x[,2],labels=rownames(pc$x),cex=0.7)

Look at association between GWG, age and BMI

plot(samplesheet$Age, samplesheet$GWG)

cor.test(samplesheet$Age, samplesheet$GWG, method="pearson")
## 
##  Pearson's product-moment correlation
## 
## data:  samplesheet$Age and samplesheet$GWG
## t = -0.051491, df = 22, p-value = 0.9594
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.4125471  0.3941649
## sample estimates:
##         cor 
## -0.01097728
cor.test(samplesheet$Age, samplesheet$GWG, method="spearman")
## Warning in cor.test.default(samplesheet$Age, samplesheet$GWG, method =
## "spearman"): Cannot compute exact p-value with ties
## 
##  Spearman's rank correlation rho
## 
## data:  samplesheet$Age and samplesheet$GWG
## S = 2219.2, p-value = 0.8706
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
##        rho 
## 0.03511084
plot(samplesheet$BMI_1, samplesheet$GWG)

cor.test(samplesheet$BMI, samplesheet$GWG, method="pearson")
## 
##  Pearson's product-moment correlation
## 
## data:  samplesheet$BMI and samplesheet$GWG
## t = 1.3509, df = 22, p-value = 0.1904
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.1425404  0.6118548
## sample estimates:
##       cor 
## 0.2767707
cor.test(samplesheet$BMI, samplesheet$GWG, method="spearman")
## Warning in cor.test.default(samplesheet$BMI, samplesheet$GWG, method =
## "spearman"): Cannot compute exact p-value with ties
## 
##  Spearman's rank correlation rho
## 
## data:  samplesheet$BMI and samplesheet$GWG
## S = 1680.6, p-value = 0.2032
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
##       rho 
## 0.2692907

Read amplicon features

bed <- read.table("amplicons_hg38.bed")

amp <- GRanges(seqnames=bed$V1,ranges=IRanges(bed$V2,bed$V3))

amp$gene_names <- bed$V4

Statistical analysis

dm <- calculateDiffMeth(meth)
## more than two groups detected:
##  will calculate methylation difference as the difference of max(x) - min(x),
##  where x is vector of mean methylation per group per region,but 
##  the statistical test will remain the same.
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
dm
##     chr     start       end strand       pvalue       qvalue   meth.diff
## 1    17  78358500  78358500      + 1.747775e-11 2.484034e-11 23.99751483
## 2    17  78358506  78358506      + 1.717842e-19 5.921350e-19 24.50901836
## 3    17  78358514  78358514      + 1.015642e-03 4.376110e-04 32.20146116
## 4    17  78358539  78358539      + 2.022724e-05 1.255407e-05 15.83878261
## 5    17  78358556  78358556      + 1.075868e-05 7.236067e-06 26.10267924
## 6    17  78358581  78358581      + 1.459061e-04 7.450872e-05 27.47895893
## 7    17  78358587  78358587      + 4.220954e-17 1.163960e-16 24.87245077
## 8     2  25161599  25161599      + 5.913814e-01 1.443167e-01 13.71794872
## 9     2  25161616  25161616      + 1.931239e-01 5.325539e-02  1.06158246
## 10    2  25161619  25161619      + 3.041524e-12 4.933666e-12 12.16709088
## 11    2  25161623  25161623      + 4.212538e-17 1.163960e-16 17.90241924
## 12    2  25161628  25161628      + 1.576361e-02 5.795914e-03 17.82101495
## 13    2  25161637  25161637      + 5.969193e-11 7.482046e-11 12.88020529
## 14    2  25161653  25161653      + 1.371105e-14 2.908405e-14 18.68001982
## 15    2  25161661  25161661      + 1.022510e-07 8.811400e-08 26.55204114
## 16    2  25161671  25161671      + 1.286359e-19 5.067474e-19 22.44093960
## 17    2  25161686  25161686      + 1.164298e-16 2.918765e-16 25.76099134
## 18    2  25161689  25161689      + 2.277120e-01 6.156207e-02 26.57811571
## 19    2  25161699  25161699      + 6.179967e-06 4.484665e-06 42.83872687
## 20    2  25161716  25161716      + 1.801607e-11 2.484034e-11 21.06120636
## 21    2  25161720  25161720      + 1.144600e-24 1.052107e-23 18.43231761
## 22    2  25161728  25161728      + 2.702916e-14 4.968997e-14 23.00876180
## 23    2  25161742  25161742      + 3.127494e-05 1.724860e-05 17.98780805
## 24    2  25161764  25161764      + 8.989406e-01 2.100760e-01 10.32084263
## 25    2  25161766  25161766      + 3.717203e-04 1.708411e-04 15.22041456
## 26    2  25161785  25161785      + 3.030813e-33 4.178848e-32 13.93065932
## 27    2  25161792  25161792      + 4.477479e-02 1.452587e-02 15.32270736
## 28    2  25161799  25161799      + 4.277064e-01 1.072212e-01  7.38753209
## 29    2  25161804  25161804      + 3.244215e-04 1.569503e-04  7.78702876
## 30    2  25161811  25161811      + 5.520543e-03 2.174759e-03 11.09382014
## 31    2  25161813  25161813      + 9.980054e-02 2.927740e-02  0.11474469
## 32    2  25161817  25161817      + 8.188786e-04 3.584317e-04  0.19860973
## 33    2  25161825  25161825      + 9.539431e-02 2.890737e-02  0.17391304
## 34    5    865252    865252      + 2.711336e-06 2.076865e-06 79.08156620
## 35    5    865254    865254      + 2.117197e-02 7.582249e-03  2.25669958
## 36    5    865278    865278      + 4.430813e-01 1.100748e-01 13.19224561
## 37    5    865296    865296      + 3.706773e-02 1.261939e-02 97.70229770
## 38    5    865349    865349      + 2.094394e-05 1.255533e-05 17.23415561
## 39    5    865357    865357      + 1.802835e-05 1.156152e-05 17.12494615
## 40    5    865391    865391      + 2.464424e-01 6.597899e-02  3.95800374
## 41    5    865394    865394      + 4.224430e-09 4.480456e-09  4.96001791
## 42    5    865435    865435      + 9.929705e-02 2.927740e-02  6.59029476
## 43    5    865441    865441      + 2.048658e-05 1.255407e-05  7.43243243
## 44    5    865466    865466      + 4.753437e-03 1.927641e-03  7.55321233
## 45    5    865469    865469      + 9.526198e-01 2.189101e-01  9.18016691
## 46    5    865473    865473      + 3.660352e-01 9.260274e-02  5.25114155
## 47    5    865480    865480      + 6.998668e-09 7.088236e-09  4.81522956
## 48    5    865483    865483      + 7.001578e-01 1.678903e-01  0.08206812
## 49    5    865485    865485      + 1.040949e-01 3.021574e-02  0.30165913
## 50    5  10649447  10649447      + 3.966125e-02 1.317698e-02  4.61538462
## 51    5  10649449  10649449      + 3.140769e-01 8.170670e-02  0.48407023
## 52    5  10649486  10649486      + 1.674053e-14 3.297378e-14  6.61659024
## 53    5  10649495  10649495      + 1.590719e-52 4.386529e-51 34.85214074
## 54    5  10649503  10649503      + 6.398242e-12 9.802021e-12  5.39802562
## 55    5  10649506  10649506      + 3.367847e-01 8.679525e-02  0.10621349
## 56    5  10649508  10649508      + 2.598808e-12 4.479005e-12  0.10605860
## 57    5 131945728 131945728      + 5.942322e-03 2.307944e-03  0.22624434
## 58    5 131945736 131945736      + 6.857500e-02 2.148872e-02  0.25706941
## 59    5 131945738 131945738      + 3.942572e-02 1.317698e-02  0.28694405
## 60    5 131945745 131945745      + 8.215229e-02 2.545406e-02 38.99782135
## 61    5 131945789 131945789      + 2.523604e-01 6.691375e-02  1.60615693
## 62    6  31575257  31575257      + 5.569945e-01 1.371388e-01 16.82074987
## 63    6  31575316  31575316      + 1.453380e-04 7.450872e-05 11.69862600
## 64    6  31575322  31575322      + 3.219596e-02 1.123833e-02 21.46261574
## 65    6  31575391  31575391      + 8.524629e-01 2.009172e-01 19.07981968
## 66    6  31575397  31575397      + 2.532721e-02 8.954066e-03 26.18230525
## 67    6  31575399  31575399      + 2.091433e-03 8.738312e-04 20.93227144
## 68    6  31575414  31575414      + 1.837600e-01 5.170737e-02 29.69585630
## 69    6  31575441  31575441      + 1.717072e-04 8.609010e-05 31.82677571
## 70    7  24283574  24283574      + 2.391154e-05 1.373706e-05 18.33333333
## 71    7  24283578  24283578      + 3.571473e-01 9.119081e-02  4.04040404
## 72    7  24283596  24283596      + 2.955606e-05 1.663328e-05 17.85714286
## 73    7  24283618  24283618      + 1.057147e-02 3.993374e-03 21.66666667
## 74    7  24283628  24283628      + 9.516755e-05 5.145720e-05 27.58620690
## 75    7  24283641  24283641      + 2.637720e-06 2.076865e-06 29.82456140
## 76    7  24283672  24283672      + 6.252170e-02 1.981705e-02 32.75862069
## 77    7  24283696  24283696      + 4.192660e-09 4.480456e-09 26.66666667
## 78    7  24283698  24283698      + 1.784551e-21 9.842068e-21 38.54166667
## 79    7  24283710  24283710      + 2.087670e-23 1.439227e-22 43.00518135
## 80    7  24283713  24283713      + 7.843962e-01 1.864683e-01 22.80701754
## 81    7  24283722  24283722      + 7.197285e-09 7.088236e-09 26.22950820
## 82    7  24283724  24283724      + 3.597779e-04 1.681551e-04 27.41935484
## 83    7  24283731  24283731      + 1.488017e-08 1.414937e-08 26.66666667
## 84    7  24283776  24283776      + 5.074496e-03 2.028015e-03 29.50819672
## 85    7  24283820  24283820      + 9.385379e-01 2.174865e-01  2.20777593
## 86    7  24283854  24283854      + 3.096397e-01 8.131952e-02  2.68745408
## 87    7  24283859  24283859      + 1.384090e-02 5.157748e-03  3.37339238
## 88    7  24283894  24283894      + 1.938701e-03 8.224793e-04  3.61023446
## 89    7  24283905  24283905      + 9.825962e-01 2.239325e-01  2.49640809
## 90    7 128241074 128241074      + 8.975436e-02 2.750050e-02 25.54652555
## 91    7 128241076 128241076      + 1.724894e-02 6.258587e-03 18.02216539
## 92    7 128241078 128241078      + 8.430188e-06 5.811720e-06 22.38217652
## 93    7 128241090 128241090      + 1.222479e-06 1.021539e-06 17.50000000
## 94    7 128241092 128241092      + 5.913447e-02 1.896137e-02 17.12817585
## 95    7 128241095 128241095      + 1.789265e-09 2.055847e-09 29.96738335
## 96    7 128241108 128241108      + 3.947845e-06 2.942293e-06 15.05336079
## 97    7 128241116 128241116      + 8.097593e-03 3.101351e-03 26.24089253
## 98    7 128241118 128241118      + 4.194429e-04 1.865558e-04 13.36064713
## 99    7 128241132 128241132      + 3.543637e-02 1.221481e-02 12.68037518
## 100   7 128241151 128241151      + 4.418805e-08 4.061730e-08  8.42450300
## 101   7 128241155 128241155      + 8.064172e-08 7.173409e-08 11.23366013
## 102   7 128241160 128241160      + 6.468962e-11 7.755936e-11  8.91891892
## 103   7 128241163 128241163      + 9.660211e-02 2.895518e-02 15.32945736
## 104   7 128241178 128241178      + 6.697058e-01 1.619969e-01 24.61523663
## 105   7 128241183 128241183      + 1.290226e-04 6.842108e-05 11.05832629
## 106   7 128241193 128241193      + 1.142776e-01 3.282596e-02 15.98173516
## 107   7 128241204 128241204      + 9.650213e-15 2.217599e-14 20.30030030
## 108   7 128241207 128241207      + 2.077847e-01 5.673090e-02 20.21473159
## 109   7 128241216 128241216      + 8.150272e-06 5.762818e-06 18.45776772
## 110   7 128241227 128241227      + 4.257322e-02 1.397606e-02 41.53129479
## 111   7 128241240 128241240      + 1.341440e-01 3.813528e-02 24.22222222
## 112   7 128241245 128241245      + 1.111420e-05 7.297200e-06 24.44901945
## 113   7 128241259 128241259      + 3.516346e-04 1.671826e-04 28.34880637
## 114   7 128241277 128241277      + 3.045543e-11 3.999198e-11 12.39731262
## 115   7 128241286 128241286      + 1.916753e-01 5.325539e-02 27.41402116
## 116   7 128241291 128241291      + 3.782331e-04 1.709847e-04 21.03383459
## 117   7 128241297 128241297      + 1.876828e-06 1.522204e-06 23.63636364
## 118   7 128241316 128241316      + 2.184010e-05 1.281399e-05 24.33333333
## 119   7 128241319 128241319      + 2.872723e-04 1.414598e-04 35.09801687
## 120   7 128241321 128241321      + 2.215289e-03 9.117653e-04 24.26501035
## 121   8  22055661  22055661      + 2.808569e-21 1.290807e-20 23.26175098
dm$pvalue<0.05
##   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE
##  [13]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE
##  [25]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE
##  [37]  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE
##  [49] FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE
##  [61] FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE
##  [73]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE
##  [85] FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE
##  [97]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE
## [109]  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE
## [121]  TRUE
min(dm$pvalue)
## [1] 1.590719e-52
plot(dm$meth.diff,-log10(dm$pvalue) )

hist(dm$meth.diff)

#dm.hyper=getMethylDiff(dm,difference=1,qvalue=0.01,type="hyper")

#dm.hypo=getMethylDiff(dm,difference=1,qvalue=0.01,type="hypo")

Lets run a simple correlation test of GWG with Beta vals

Here we run a spearman correlation test of the assocation between GWG and beta vals.

z <- samplesheet$GWG

genes <- amp

genes %>% kbl() %>% kable_styling()
seqnames start end width strand gene_names
17 78358469 78358619 151
SOCS3
2 25161598 25161833 236
POMC_2
2 25168373 25168611 239
POMC_1
6 31575210 31575467 258
TNF
7 24283548 24283843 296
NPY_1
7 24283796 24283936 141
NPY_2
7 128241036 128241347 312
LEP
par(mfrow=c(1,1))
x <- lapply( 1:nrow(meth), function(i) {
  x <- as.vector(percMethylation(meth)[i,])
  cor <- cor.test(x,z,method="pearson")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

  #plot(z,x,xlab="GWG",ylab="Beta",main="Pearson")
  #mtext(HEADER)
  #mylm <- lm( x ~ z )
  #abline(mylm,lwd=3,lty=2,col="red")

  cor <- cor.test(x,z,method="spearman")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

  plot(rank(z),rank(x),xlab="rank(GWG)",ylab="rank(Beta)",main="Spearman")
  mtext(HEADER)
  mylm <- lm( rank(x) ~ rank(z) )
  abline(mylm,lwd=3,lty=2,col="red")

  c("p"=p,"r"=r)
})
## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

Now let’s present the results.

xx <- as.data.frame(t(sapply(x,function(x){ x[c(2,1)] } )))
xx$FDR <- p.adjust(xx[,2],method="fdr")
xx <- data.frame(meth$chr,meth$start,xx)
colnames(xx) <- c("seqname","pos","rho","p","FDR")

gr <- GRanges(seqnames = xx$seqname, ranges = IRanges(xx$pos) )
gr$r <- xx$r
gr$p <- xx$p
gr$FDR <- xx$FDR

ol <- findOverlaps(gr,genes)

# off target gene methylation
ot <- gr[-queryHits(ol)]
ot %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR
5 865252 865252 1
0.2305193 0.2784972 0.8498154
5 865254 865254 1
-0.4191261 0.0414860 0.5639518
5 865278 865278 1
0.0008732 0.9967691 0.9967691
5 865296 865296 1
0.0794593 0.7120731 0.9399774
5 865349 865349 1
-0.1934092 0.3651909 0.9399774
5 865357 865357 1
-0.3152177 0.1335208 0.6462409
5 865391 865391 1
0.1174426 0.5847003 0.9399774
5 865394 865394 1
-0.2693758 0.2030520 0.7445241
5 865435 865435 1
-0.0781495 0.7166267 0.9399774
5 865441 865441 1
0.2938248 0.1634429 0.6618646
5 865466 865466 1
-0.1938458 0.3640885 0.9399774
5 865469 865469 1
0.0571932 0.7906643 0.9427970
5 865473 865473 1
-0.1458209 0.4965765 0.9399774
5 865480 865480 1
0.3056128 0.1464245 0.6561988
5 865483 865483 1
-0.1078497 0.6159382 0.9399774
5 865485 865485 1
0.2003400 0.3479198 0.9399774
5 10649447 10649447 1
0.0235964 0.9128520 0.9604790
5 10649449 10649449 1
0.2938248 0.1634429 0.6618646
5 10649486 10649486 1
0.1484405 0.4887891 0.9399774
5 10649495 10649495 1
-0.0803325 0.7090426 0.9399774
5 10649503 10649503 1
-0.1060913 0.6217372 0.9399774
5 10649506 10649506 1
-0.1604138 0.4539892 0.9399774
5 10649508 10649508 1
-0.3478499 0.0957889 0.5639518
5 131945728 131945728 1
-0.3478499 0.0957889 0.5639518
5 131945736 131945736 1
0.2299217 0.2797799 0.8498154
5 131945738 131945738 1
-0.3928341 0.0575779 0.5639518
5 131945745 131945745 1
0.1648761 0.4413609 0.9399774
5 131945789 131945789 1
0.0960497 0.6552644 0.9399774
8 22055661 22055661 1
-0.1768188 0.4085028 0.9399774
# on target methylation
gr <- gr[queryHits(ol)]

gr$gene_names <- genes$gene_names[subjectHits(ol) ]

gr %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR gene_names
17 78358500 78358500 1
0.3353009 0.1092206 0.5639518 SOCS3
17 78358506 78358506 1
0.0440956 0.8378923 0.9427970 SOCS3
17 78358514 78358514 1
0.1309769 0.5418376 0.9399774 SOCS3
17 78358539 78358539 1
0.2300827 0.2794339 0.8498154 SOCS3
17 78358556 78358556 1
0.0794593 0.7120731 0.9399774 SOCS3
17 78358581 78358581 1
0.2458000 0.2469636 0.8498154 SOCS3
17 78358587 78358587 1
-0.1886067 0.3774446 0.9399774 SOCS3
2 25161599 25161599 1
0.1466941 0.4939739 0.9399774 POMC_2
2 25161616 25161616 1
0.0471517 0.8268175 0.9427970 POMC_2
2 25161619 25161619 1
0.2719954 0.1985233 0.7445241 POMC_2
2 25161623 25161623 1
0.0825154 0.7014852 0.9399774 POMC_2
2 25161628 25161628 1
-0.0846984 0.6939552 0.9399774 POMC_2
2 25161637 25161637 1
0.1510600 0.4810633 0.9399774 POMC_2
2 25161653 25161653 1
0.0314345 0.8840703 0.9466593 POMC_2
2 25161661 25161661 1
0.3383570 0.1058289 0.5639518 POMC_2
2 25161671 25161671 1
0.0048025 0.9822315 0.9967691 POMC_2
2 25161686 25161686 1
-0.0152806 0.9435035 0.9749080 POMC_2
2 25161689 25161689 1
0.1122035 0.6016759 0.9399774 POMC_2
2 25161699 25161699 1
-0.1741993 0.4155914 0.9399774 POMC_2
2 25161716 25161716 1
-0.1536796 0.4733999 0.9399774 POMC_2
2 25161720 25161720 1
-0.1803115 0.3991563 0.9399774 POMC_2
2 25161728 25161728 1
-0.0720373 0.7379988 0.9399774 POMC_2
2 25161742 25161742 1
0.0571932 0.7906643 0.9427970 POMC_2
2 25161764 25161764 1
0.0969229 0.6523220 0.9399774 POMC_2
2 25161766 25161766 1
-0.0013098 0.9951537 0.9967691 POMC_2
2 25161785 25161785 1
0.3108518 0.1392807 0.6481907 POMC_2
2 25161792 25161792 1
-0.0502078 0.8157746 0.9427970 POMC_2
2 25161799 25161799 1
0.0585030 0.7859777 0.9427970 POMC_2
2 25161804 25161804 1
-0.0397297 0.8537650 0.9427970 POMC_2
2 25161811 25161811 1
-0.2261534 0.2879540 0.8498154 POMC_2
2 25161813 25161813 1
0.1341203 0.5320960 0.9399774 POMC_2
2 25161817 25161817 1
-0.3569757 0.0868225 0.5639518 POMC_2
2 25161825 25161825 1
0.0848181 0.6935432 0.9399774 POMC_2
6 31575257 31575257 1
0.1458209 0.4965765 0.9399774 TNF
6 31575316 31575316 1
0.1571723 0.4632800 0.9399774 TNF
6 31575322 31575322 1
-0.0366815 0.8648799 0.9427970 TNF
6 31575391 31575391 1
-0.0144075 0.9467273 0.9749080 TNF
6 31575397 31575397 1
-0.0488980 0.8205032 0.9427970 TNF
6 31575399 31575399 1
0.1126401 0.6002534 0.9399774 TNF
6 31575414 31575414 1
-0.2383780 0.2619761 0.8498154 TNF
6 31575441 31575441 1
-0.1161328 0.5889247 0.9399774 TNF
7 24283574 24283574 1
-0.1655748 0.4394009 0.9399774 NPY_1
7 24283578 24283578 1
-0.0766178 0.7219640 0.9399774 NPY_1
7 24283596 24283596 1
-0.0552148 0.7977568 0.9427970 NPY_1
7 24283618 24283618 1
0.0422370 0.8446420 0.9427970 NPY_1
7 24283628 24283628 1
0.0269067 0.9006813 0.9559863 NPY_1
7 24283641 24283641 1
0.0847511 0.6937737 0.9399774 NPY_1
7 24283672 24283672 1
0.0751406 0.7271230 0.9399774 NPY_1
7 24283696 24283696 1
-0.3958763 0.0555014 0.5639518 NPY_1
7 24283698 24283698 1
-0.1206670 0.5743568 0.9399774 NPY_1
7 24283710 24283710 1
-0.4426874 0.0302883 0.5639518 NPY_1
7 24283713 24283713 1
-0.3527195 0.0909225 0.5639518 NPY_1
7 24283722 24283722 1
-0.1581808 0.4603787 0.9399774 NPY_1
7 24283724 24283724 1
-0.0872307 0.6852553 0.9399774 NPY_1
7 24283731 24283731 1
-0.2837018 0.1791257 0.6991682 NPY_1
7 24283776 24283776 1
0.0399167 0.8530838 0.9427970 NPY_1
7 24283820 24283820 1
0.1226817 0.5679352 0.9399774 NPY_1
7 24283820 24283820 1
0.1226817 0.5679352 0.9399774 NPY_2
7 24283854 24283854 1
-0.1283574 0.5500185 0.9399774 NPY_2
7 24283859 24283859 1
-0.0925570 0.6670834 0.9399774 NPY_2
7 24283894 24283894 1
-0.1327233 0.5364152 0.9399774 NPY_2
7 24283905 24283905 1
0.0724739 0.7364658 0.9399774 NPY_2
7 128241074 128241074 1
-0.0462785 0.8299786 0.9427970 LEP
7 128241076 128241076 1
-0.1392721 0.5163106 0.9399774 LEP
7 128241078 128241078 1
-0.3929307 0.0575111 0.5639518 LEP
7 128241090 128241090 1
-0.4012259 0.0519912 0.5639518 LEP
7 128241092 128241092 1
-0.0803325 0.7090426 0.9399774 LEP
7 128241095 128241095 1
-0.3329720 0.1118582 0.5639518 LEP
7 128241108 128241108 1
-0.4894170 0.0152117 0.5639518 LEP
7 128241116 128241116 1
-0.0340540 0.8744811 0.9447519 LEP
7 128241118 128241118 1
-0.3387936 0.1053508 0.5639518 LEP
7 128241132 128241132 1
-0.1693968 0.4287609 0.9399774 LEP
7 128241151 128241151 1
-0.2933882 0.1640987 0.6618646 LEP
7 128241155 128241155 1
-0.3366106 0.1077574 0.5639518 LEP
7 128241160 128241160 1
-0.3593133 0.0846306 0.5639518 LEP
7 128241163 128241163 1
-0.0969229 0.6523220 0.9399774 LEP
7 128241178 128241178 1
-0.0133218 0.9507367 0.9749080 LEP
7 128241183 128241183 1
-0.3772135 0.0692002 0.5639518 LEP
7 128241193 128241193 1
-0.0585540 0.7857956 0.9427970 LEP
7 128241204 128241204 1
-0.4344067 0.0339087 0.5639518 LEP
7 128241207 128241207 1
-0.0373365 0.8624892 0.9427970 LEP
7 128241216 128241216 1
-0.3488351 0.0947890 0.5639518 LEP
7 128241227 128241227 1
-0.1259835 0.5574806 0.9399774 LEP
7 128241240 128241240 1
-0.1039083 0.6289668 0.9399774 LEP
7 128241245 128241245 1
-0.2309559 0.2775624 0.8498154 LEP
7 128241259 128241259 1
-0.1846774 0.3876434 0.9399774 LEP
7 128241277 128241277 1
-0.4082113 0.0476702 0.5639518 LEP
7 128241286 128241286 1
-0.0410394 0.8489971 0.9427970 LEP
7 128241291 128241291 1
-0.4239286 0.0389736 0.5639518 LEP
7 128241297 128241297 1
-0.2076887 0.3301456 0.9399774 LEP
7 128241316 128241316 1
-0.4941086 0.0141222 0.5639518 LEP
7 128241319 128241319 1
-0.2265900 0.2869994 0.8498154 LEP
7 128241321 128241321 1
-0.5234710 0.0086622 0.5639518 LEP

Remove outliers

Two samples (pool8, pool17) showed unusual profiles that are consistent with incomplete bisulfite conversion.

file.list <- file.list[which(! file.list %in% c("pool8","pool17"))]

samplesheet <- samplesheet[which(! samplesheet$poolID %in% c("pool8","pool17")),]


myobj <- methRead( location=as.list(paste("fastq/",file.list,".methylkit.tsv",sep="")),
  sample.id=as.list(samplesheet$poolID),
  header=FALSE,
  assembly="hg38",
  treatment=samplesheet$GWG,
  context="CpG",
  mincov = 5 )
## Received list of locations.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
## Reading file.
myobjf <- filterByCoverage(myobj,lo.count=5,lo.perc=NULL,
  hi.count=NULL,hi.perc=NULL)

meth <- unite(myobjf, destrand=FALSE)
## uniting...

Now run a spearman correlation test of GWG with Beta vals.

Have modified the script so it doesn’t plot the pearson values.

z <- samplesheet$GWG

genes <- amp

genes %>% kbl() %>% kable_styling()
seqnames start end width strand gene_names
17 78358469 78358619 151
SOCS3
2 25161598 25161833 236
POMC_2
2 25168373 25168611 239
POMC_1
6 31575210 31575467 258
TNF
7 24283548 24283843 296
NPY_1
7 24283796 24283936 141
NPY_2
7 128241036 128241347 312
LEP
par(mfrow=c(1,1))
x <- lapply( 1:nrow(meth), function(i) {
  x <- as.vector(percMethylation(meth)[i,])
  cor <- cor.test(x,z,method="pearson")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

#  plot(z,x,xlab="GWG",ylab="Beta",main="Pearson")
#  mtext(HEADER)
#  mylm <- lm( x ~ z )
#  abline(mylm,lwd=3,lty=2,col="red")

  cor <- cor.test(x,z,method="spearman")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

  plot(rank(z),rank(x),xlab="rank(GWG)",ylab="rank(Beta)",main="Spearman")
  mtext(HEADER)
  mylm <- lm( rank(x) ~ rank(z) )
  abline(mylm,lwd=3,lty=2,col="red")

  c("p"=p,"r"=r)
})
## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

xx <- as.data.frame(t(sapply(x,function(x){ x[c(2,1)] } )))
xx$FDR <- p.adjust(xx[,2],method="fdr")
xx <- data.frame(meth$chr,meth$start,xx)
colnames(xx) <- c("seqname","pos","rho","p","FDR")

gr <- GRanges(seqnames = xx$seqname, ranges = IRanges(xx$pos) )
gr$r <- xx$r
gr$p <- xx$p
gr$FDR <- xx$FDR

ol <- findOverlaps(gr,genes)

# off target gene methylation
ot <- gr[-queryHits(ol)]
ot %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR
16 14989709 14989709 1
-0.1591335 0.4793424 0.9090315
16 14989712 14989712 1
0.1204899 0.5932645 0.9090315
16 14989741 14989741 1
-0.2533304 0.2553109 0.8531121
16 14989762 14989762 1
-0.1627177 0.4693685 0.9090315
16 14989764 14989764 1
-0.1797546 0.4234437 0.9090315
16 14989771 14989771 1
0.2595660 0.2433981 0.8531121
16 14989775 14989775 1
0.1391830 0.5367482 0.9090315
16 14989785 14989785 1
-0.0584577 0.7960933 0.9321776
16 14989801 14989801 1
-0.1106982 0.6238336 0.9090315
16 14989804 14989804 1
0.1521988 0.4989383 0.9090315
16 14989809 14989809 1
-0.2158716 0.3346122 0.9090315
16 14989812 14989812 1
-0.0009303 0.9967218 0.9967218
16 14989820 14989820 1
0.0672026 0.7663560 0.9309958
16 14989827 14989827 1
-0.0332202 0.8833205 0.9785880
16 14989844 14989844 1
0.1124376 0.6183575 0.9090315
16 14989857 14989857 1
0.0854367 0.7054051 0.9090315
5 865252 865252 1
0.3269988 0.1374321 0.7238218
5 865254 865254 1
-0.3457331 0.1150198 0.7238218
5 865278 865278 1
-0.0164635 0.9420308 0.9785880
5 865296 865296 1
0.0232760 0.9181100 0.9785880
5 865349 865349 1
-0.2986135 0.1770467 0.7485262
5 865357 865357 1
-0.3173478 0.1501172 0.7238218
5 865391 865391 1
0.0885622 0.6951190 0.9090315
5 865394 865394 1
-0.2202700 0.3246148 0.9090315
5 865435 865435 1
-0.0079479 0.9719974 0.9811587
5 865441 865441 1
0.3298373 0.1338509 0.7238218
5 865466 865466 1
-0.2895302 0.1912293 0.7485262
5 865469 865469 1
0.1254631 0.5779855 0.9090315
5 865473 865473 1
-0.0607446 0.7882885 0.9309958
5 865480 865480 1
0.3099676 0.1603576 0.7322998
5 865483 865483 1
-0.0922550 0.6830324 0.9090315
5 865485 865485 1
0.1729417 0.4415102 0.9090315
5 10649447 10649447 1
0.0346693 0.8782669 0.9785880
5 10649449 10649449 1
0.4235089 0.0495251 0.7238218
5 10649486 10649486 1
0.1504422 0.5039636 0.9090315
5 10649495 10649495 1
-0.0215728 0.9240846 0.9785880
5 10649503 10649503 1
-0.1396557 0.5353520 0.9090315
5 10649506 10649506 1
-0.1940489 0.3868689 0.9090315
5 10649508 10649508 1
-0.3285286 0.1354936 0.7238218
5 131945728 131945728 1
-0.3631106 0.0967183 0.7238218
5 131945736 131945736 1
0.2180120 0.3297245 0.9090315
5 131945738 131945738 1
-0.4800902 0.0237408 0.5420813
5 131945745 131945745 1
0.2934628 0.1849974 0.7485262
5 131945789 131945789 1
0.0840205 0.7100822 0.9090315
8 22055661 22055661 1
-0.1669056 0.4578502 0.9090315
# on target methylation
gr <- gr[queryHits(ol)]

gr$gene_names <- genes$gene_names[subjectHits(ol) ]

gr %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR gene_names
17 78358500 78358500 1
0.2634157 0.2362265 0.8516588 SOCS3
17 78358506 78358506 1
-0.0874268 0.6988498 0.9090315 SOCS3
17 78358514 78358514 1
0.1044579 0.6436361 0.9090315 SOCS3
17 78358539 78358539 1
0.1884785 0.4009050 0.9090315 SOCS3
17 78358556 78358556 1
-0.0141927 0.9500161 0.9785880 SOCS3
17 78358581 78358581 1
0.1612286 0.4734994 0.9090315 SOCS3
17 78358587 78358587 1
-0.3514102 0.1087848 0.7238218 SOCS3
2 25161599 25161599 1
0.1424943 0.5270047 0.9090315 POMC_2
2 25161616 25161616 1
0.0908330 0.6876780 0.9090315 POMC_2
2 25161619 25161619 1
0.3150770 0.1532178 0.7238218 POMC_2
2 25161623 25161623 1
0.1288693 0.5676203 0.9090315 POMC_2
2 25161628 25161628 1
-0.0868591 0.7007177 0.9090315 POMC_2
2 25161637 25161637 1
0.0885622 0.6951190 0.9090315 POMC_2
2 25161653 25161653 1
0.0993486 0.6600264 0.9090315 POMC_2
2 25161661 25161661 1
0.3627643 0.0970606 0.7238218 POMC_2
2 25161671 25161671 1
0.1277339 0.5710662 0.9090315 POMC_2
2 25161686 25161686 1
0.1214891 0.5901809 0.9090315 POMC_2
2 25161689 25161689 1
0.2123221 0.3428117 0.9090315 POMC_2
2 25161699 25161699 1
-0.0760726 0.7365146 0.9090315 POMC_2
2 25161716 25161716 1
-0.0073802 0.9739969 0.9811587 POMC_2
2 25161720 25161720 1
-0.0266822 0.9061740 0.9785880 POMC_2
2 25161728 25161728 1
0.0283853 0.9002132 0.9785880 POMC_2
2 25161742 25161742 1
0.2316241 0.2996483 0.9090315 POMC_2
2 25161764 25161764 1
0.2049420 0.3602355 0.9090315 POMC_2
2 25161766 25161766 1
0.1203537 0.5936852 0.9090315 POMC_2
2 25161785 25161785 1
0.4110193 0.0573960 0.7238218 POMC_2
2 25161792 25161792 1
0.0936715 0.6784158 0.9090315 POMC_2
2 25161799 25161799 1
0.0800466 0.7232603 0.9090315 POMC_2
2 25161804 25161804 1
-0.0789112 0.7270396 0.9090315 POMC_2
2 25161811 25161811 1
-0.1663379 0.4594030 0.9090315 POMC_2
2 25161813 25161813 1
0.1408842 0.5317319 0.9090315 POMC_2
2 25161817 25161817 1
-0.2558935 0.2503698 0.8531121 POMC_2
2 25161825 25161825 1
-0.0146492 0.9484103 0.9785880 POMC_2
6 31575257 31575257 1
0.1527130 0.4974719 0.9090315 TNF
6 31575316 31575316 1
0.1362495 0.5454491 0.9090315 TNF
6 31575322 31575322 1
-0.1862602 0.4065719 0.9090315 TNF
6 31575391 31575391 1
0.0295207 0.8962421 0.9785880 TNF
6 31575397 31575397 1
0.0107864 0.9620026 0.9811587 TNF
6 31575399 31575399 1
0.2793115 0.2080842 0.7704739 TNF
6 31575414 31575414 1
-0.2333273 0.2960082 0.9090315 TNF
6 31575441 31575441 1
-0.0465519 0.8370148 0.9616715 TNF
7 24283574 24283574 1
-0.0610743 0.7871648 0.9309958 NPY_1
7 24283578 24283578 1
0.0185542 0.9346835 0.9785880 NPY_1
7 24283596 24283596 1
0.0395145 0.8614031 0.9753077 NPY_1
7 24283618 24283618 1
0.1663276 0.4594312 0.9090315 NPY_1
7 24283628 24283628 1
0.0205792 0.9275723 0.9785880 NPY_1
7 24283641 24283641 1
0.2011085 0.3694845 0.9090315 NPY_1
7 24283672 24283672 1
0.1946695 0.3853225 0.9090315 NPY_1
7 24283696 24283696 1
-0.3761133 0.0845000 0.7238218 NPY_1
7 24283698 24283698 1
-0.0450119 0.8423400 0.9616715 NPY_1
7 24283710 24283710 1
-0.5010097 0.0175410 0.5415473 NPY_1
7 24283713 24283713 1
-0.3378954 0.1240482 0.7238218 NPY_1
7 24283722 24283722 1
-0.1191043 0.5975515 0.9090315 NPY_1
7 24283724 24283724 1
-0.0511539 0.8211430 0.9533609 NPY_1
7 24283731 24283731 1
-0.1955349 0.3831719 0.9090315 NPY_1
7 24283776 24283776 1
-0.0625884 0.7820100 0.9309958 NPY_1
7 24283820 24283820 1
0.1283016 0.5693421 0.9090315 NPY_1
7 24283820 24283820 1
0.1283016 0.5693421 0.9090315 NPY_2
7 24283854 24283854 1
-0.1237600 0.5831987 0.9090315 NPY_2
7 24283859 24283859 1
-0.1163798 0.6060190 0.9090315 NPY_2
7 24283894 24283894 1
-0.1788275 0.4258786 0.9090315 NPY_2
7 24283905 24283905 1
0.2128898 0.3414923 0.9090315 NPY_2
7 128241074 128241074 1
-0.2083482 0.3521310 0.9090315 LEP
7 128241076 128241076 1
-0.2412752 0.2793842 0.8901311 LEP
7 128241078 128241078 1
-0.5035554 0.0168857 0.5415473 LEP
7 128241090 128241090 1
-0.3201863 0.1463039 0.7238218 LEP
7 128241092 128241092 1
-0.1101350 0.6256107 0.9090315 LEP
7 128241095 128241095 1
-0.2918834 0.1874833 0.7485262 LEP
7 128241108 128241108 1
-0.3406237 0.1208494 0.7238218 LEP
7 128241116 128241116 1
-0.0760726 0.7365146 0.9090315 LEP
7 128241118 128241118 1
-0.3565195 0.1033875 0.7238218 LEP
7 128241132 128241132 1
-0.2168638 0.3323411 0.9090315 LEP
7 128241151 128241151 1
-0.3264311 0.1381565 0.7238218 LEP
7 128241155 128241155 1
-0.4558681 0.0329863 0.6455884 LEP
7 128241160 128241160 1
-0.3758215 0.0847609 0.7238218 LEP
7 128241163 128241163 1
-0.2072128 0.3548206 0.9090315 LEP
7 128241178 128241178 1
-0.0633171 0.7795321 0.9309958 LEP
7 128241183 128241183 1
-0.3457331 0.1150198 0.7238218 LEP
7 128241193 128241193 1
-0.0880940 0.6966565 0.9090315 LEP
7 128241204 128241204 1
-0.4382692 0.0413295 0.7077678 LEP
7 128241207 128241207 1
-0.0945498 0.6755590 0.9090315 LEP
7 128241216 128241216 1
-0.2844208 0.1995369 0.7593486 LEP
7 128241227 128241227 1
-0.0868591 0.7007177 0.9090315 LEP
7 128241240 128241240 1
-0.0845882 0.7082060 0.9090315 LEP
7 128241245 128241245 1
-0.2469522 0.2678762 0.8737866 LEP
7 128241259 128241259 1
-0.3162124 0.1516619 0.7238218 LEP
7 128241277 128241277 1
-0.2895302 0.1912293 0.7485262 LEP
7 128241286 128241286 1
-0.1328433 0.5556326 0.9090315 LEP
7 128241291 128241291 1
-0.5313730 0.0109312 0.5415473 LEP
7 128241297 128241297 1
-0.1687040 0.4529493 0.9090315 LEP
7 128241316 128241316 1
-0.4929082 0.0197645 0.5415473 LEP
7 128241319 128241319 1
-0.3451654 0.1156572 0.7238218 LEP
7 128241321 128241321 1
-0.5308053 0.0110325 0.5415473 LEP

Genome landscape of methylation changes across each CPG site

Show the RHO/pval at each site, in context with the gene.

#load gene symbol : GRanges, one gene/row
data(genesymbol, package = "biovizBase")
#retrieve information of the gene of interest
wh <- genesymbol[c("LEP")]+3000
wh <- range(wh, ignore.strand = TRUE)
#Plot the different transcripts  for our gene of interest
tx_track <- autoplot(Homo.sapiens, which = wh)
## Parsing transcripts...
## Parsing exons...
## Parsing cds...
## Parsing utrs...
## ------exons...
## ------cdss...
## ------introns...
## ------utr...
## aggregating...
## Done
## 'select()' returned 1:1 mapping between keys and columns
## Constructing graphics...
seqname <- c("chr7","chr7","chr7","chr7")
starts <- c( 127885000 , 127885500, 127886000, 127886500 )
ends <- c( 127885200 , 127885700, 127886200, 127886700 )
gene_data <- GRanges(seqname, IRanges(starts, ends))
gene_data$score <- c(0.5,1,2,5)
generange <- GRanges(seqname, IRanges(127885000, 127886700))
meth_track <- autoplot( gene_data , which = generange, geom = "bar")
## use score as y by default
tracks(Genes=tx_track , Meth=meth_track, heights = c(0.3, 0.2)) + ylab("")

chainfile = system.file(package="liftOver", "extdata", "hg38ToHg19.over.chain")
ch = import.chain(chainfile)
genes2 <- genes
seqlevelsStyle(genes2) = "UCSC"  # necessary
genes19 <- liftOver(genes2, ch)
genes19 <- unlist(genes19)
genome(genes19) <- "hg19"

gr38 <- gr
seqlevelsStyle(gr38) = "UCSC"  # necessary
gr19 <- liftOver(gr38, ch)
gr19 <- unlist(gr19)
genome(gr19) <- "hg19"
ranges(gr19) <- ranges(gr19)+2

# LEP 7
generange <- genes19[7]
gr19$score <- gr19$r
gr19$sig <- as.character(as.numeric(gr19$p < 0.05))
gr19$sig <- gsub("0","gray",gr19$sig)
gr19$sig <- gsub("1","red",gr19$sig)
meth_data <- gr19[queryHits(findOverlaps(gr19,generange))]
meth_track <- autoplot( meth_data , which = generange, geom = "bar", fill= meth_data$sig )
## use score as y by default
wh <- genesymbol[c("LEP")]+3000
wh <- range(wh, ignore.strand = TRUE)
#Plot the different transcripts  for our gene of interest
tx_track <- autoplot(Homo.sapiens, which = wh)
## Parsing transcripts...
## Parsing exons...
## Parsing cds...
## Parsing utrs...
## ------exons...
## ------cdss...
## ------introns...
## ------utr...
## aggregating...
## Done
## 'select()' returned 1:1 mapping between keys and columns
## Constructing graphics...
tracks(Genes=tx_track , Meth=meth_track, heights = c(0.1, 0.2)) + ylab("")

tx_track <- autoplot(Homo.sapiens, which = generange)
## Parsing transcripts...
## Parsing exons...
## Parsing cds...
## Parsing utrs...
## ------exons...
## ------cdss...
## ------introns...
## ------utr...
## aggregating...
## Done
## 'select()' returned 1:1 mapping between keys and columns
## Constructing graphics...
tracks(Genes=tx_track , Meth=meth_track, heights = c(0.1, 0.2)) + ylab("")

# TNF 4
generange <- genes19[4]
gr19$score <- gr19$r
gr19$sig <- as.character(as.numeric(gr19$p < 0.05))
gr19$sig <- gsub("0","gray",gr19$sig)
gr19$sig <- gsub("1","red",gr19$sig)
meth_data <- gr19[queryHits(findOverlaps(gr19,generange)) ]
meth_track <- autoplot( meth_data , which = generange, geom = "bar", fill= meth_data$sig )
## use score as y by default
wh <- genesymbol[c("TNF")]+1000
wh <- range(wh, ignore.strand = TRUE)
tx_track <- autoplot(Homo.sapiens, which = wh)
## Parsing transcripts...
## Parsing exons...
## Parsing cds...
## Parsing utrs...
## ------exons...
## ------cdss...
## ------introns...
## ------utr...
## aggregating...
## Done
## 'select()' returned 1:1 mapping between keys and columns
## Constructing graphics...
tracks(Genes=tx_track , Meth=meth_track, heights = c(0.1, 0.2)) + ylab("")

# SOCS3 1
generange <- genes19[1]
gr19$score <- gr19$r
gr19$sig <- as.character(as.numeric(gr19$p < 0.05))
gr19$sig <- gsub("0","gray",gr19$sig)
gr19$sig <- gsub("1","red",gr19$sig)
meth_data <- gr19[queryHits(findOverlaps(gr19,generange)) ]
meth_track <- autoplot( meth_data , which = generange, geom = "bar", fill= meth_data$sig )
## use score as y by default
wh <- genesymbol[c("SOCS3")]+1000
wh <- range(wh, ignore.strand = TRUE)
tx_track <- autoplot(Homo.sapiens, which = wh)
## Parsing transcripts...
## Parsing exons...
## Parsing cds...
## Parsing utrs...
## ------exons...
## ------cdss...
## ------introns...
## ------utr...
## aggregating...
## Done
## 'select()' returned 1:1 mapping between keys and columns
## Constructing graphics...
tracks(Genes=tx_track , Meth=meth_track, heights = c(0.1, 0.2)) + ylab("")
## Warning: Removed 1 rows containing missing values (geom_text).

# POMC_2 2
generange <- genes19[2]
gr19$score <- gr19$r
gr19$sig <- as.character(as.numeric(gr19$p < 0.05))
gr19$sig <- gsub("0","gray",gr19$sig)
gr19$sig <- gsub("1","red",gr19$sig)
meth_data <- gr19[queryHits(findOverlaps(gr19,generange)) ]
meth_track <- autoplot( meth_data , which = generange, geom = "bar", fill= meth_data$sig )
## use score as y by default
wh <- genesymbol[c("POMC")]+1000
wh <- range(wh, ignore.strand = TRUE)
tx_track <- autoplot(Homo.sapiens, which = wh)
## Parsing transcripts...
## Parsing exons...
## Parsing cds...
## Parsing utrs...
## ------exons...
## ------cdss...
## ------introns...
## ------utr...
## aggregating...
## Done
## 'select()' returned 1:1 mapping between keys and columns
## Constructing graphics...
tracks(Genes=tx_track , Meth=meth_track, heights = c(0.1, 0.2)) + ylab("")

# NPY_1 5
generange <- genes19[5]
gr19$score <- gr19$r
gr19$sig <- as.character(as.numeric(gr19$p < 0.05))
gr19$sig <- gsub("0","gray",gr19$sig)
gr19$sig <- gsub("1","red",gr19$sig)
meth_data <- gr19[queryHits(findOverlaps(gr19,generange)) ]
meth_track <- autoplot( meth_data , which = generange, geom = "bar", fill= meth_data$sig )
## use score as y by default
wh <- genesymbol[c("NPY")]+1000
wh <- range(wh, ignore.strand = TRUE)
tx_track <- autoplot(Homo.sapiens, which = wh)
## Parsing transcripts...
## Parsing exons...
## Parsing cds...
## Parsing utrs...
## ------exons...
## ------cdss...
## ------introns...
## ------utr...
## aggregating...
## Done
## 'select()' returned 1:1 mapping between keys and columns
## Constructing graphics...
tracks(Genes=tx_track , Meth=meth_track, heights = c(0.1, 0.2)) + ylab("")

Graph of correlation coefficient and p-values across gene loci

xxgr <- GRanges(xx,seqnames=xx$seqname,ranges=IRanges(xx$pos,end=xx$pos),strand="+")

mygenenames <- unique(gr$gene_names)

sapply(mygenenames, function(mygenename) {
  mygene <- gr[gr$gene_names==mygenename,]
  myol <- findOverlaps(xxgr,mygene)
  x <- xxgr[queryHits(myol),]
  par(mfrow=c(2,1))
  par(mar=c(5,4,2,2))
  barplot(-log(x$p),names=x$pos,las=2,cex.names=0.5,ylab="-log(p) nominal",main=mygenename)
  abline(h=-log(0.05))
  barplot(x$rho,names=x$pos,las=2,cex.names=0.5,ylab="Spearman's rho")
})

## $SOCS3
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## [6,]  6.7
## [7,]  7.9
## 
## $POMC_2
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## [17,] 19.9
## [18,] 21.1
## [19,] 22.3
## [20,] 23.5
## [21,] 24.7
## [22,] 25.9
## [23,] 27.1
## [24,] 28.3
## [25,] 29.5
## [26,] 30.7
## 
## $TNF
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## [6,]  6.7
## [7,]  7.9
## [8,]  9.1
## 
## $NPY_1
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## 
## $NPY_2
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## 
## $LEP
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## [17,] 19.9
## [18,] 21.1
## [19,] 22.3
## [20,] 23.5
## [21,] 24.7
## [22,] 25.9
## [23,] 27.1
## [24,] 28.3
## [25,] 29.5
## [26,] 30.7
## [27,] 31.9
## [28,] 33.1
## [29,] 34.3
## [30,] 35.5
## [31,] 36.7

Scatterplot of GWG vs aggregated locus methylation

Need to include the formula of the association.

CHR=as.vector(seqnames(GRanges(meth)))
POS=as.character(start(ranges(GRanges(meth))))
CHRPOS=paste("chr",CHR,":",POS,sep="")

lapply(c(1,2,4:7), function(i) {

  gene <- genes[i]
  gname <- genes[i]$gene_names
  myrows <- subjectHits( findOverlaps( gene , GRanges(getData(meth)[,1:3] )) )
  betas <- percMethylation(meth)[myrows,]
  cm <- colMeans(betas)
  ct <- cor.test(cm,z,method="s")
  mylm <- lm( cm ~ z )

  SUBHEADER=paste( "Int=",signif(mylm$coefficients[1],3),
    ", slope=",signif(mylm$coefficients[2],3),
    ", r2adj=",signif(summary(mylm)$adj.r.squared,3),
    ", rho=",signif(ct$est,3),
    ", p=",signif(ct$p.value,3), sep="")

  plot(z,cm,pch=19,xlab="GWG (kg)",ylab="% methylation",main=gname)
  abline(mylm,lwd=3,lty=2,col="red")
  mtext(SUBHEADER)

})
## Warning in cor.test.default(cm, z, method = "s"): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(cm, z, method = "s"): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(cm, z, method = "s"): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(cm, z, method = "s"): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(cm, z, method = "s"): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(cm, z, method = "s"): Cannot compute exact p-value
## with ties

## [[1]]
## NULL
## 
## [[2]]
## NULL
## 
## [[3]]
## NULL
## 
## [[4]]
## NULL
## 
## [[5]]
## NULL
## 
## [[6]]
## NULL

Permutation test

Here I’m going to resample the existing p-value data with random methylation direction.

From that distribution I can estimate the

scores <- -log10(gr$p) * sample(c(-1,1),length(gr$p),replace=TRUE)

npermutes = 10000

permute_res <- sapply(mygenenames, function(mygenename) {
  mygene <- gr[gr$gene_names==mygenename,]
  myol <- findOverlaps(xxgr,mygene)
  x <- xxgr[queryHits(myol),]
  xscore <- mean(-log10(x$p) * as.data.frame(x)[,8])
  permutes <- replicate(n=npermutes ,  mean( -log10(gr$p) * sample(c(-1,1),length(gr$p),replace=TRUE ) ) )
  greaterthan <- length(which(permutes > xscore))
  lessthan <- length(which(permutes < xscore))
  p_greater = greaterthan / ( greaterthan + lessthan )
  p_less = lessthan / ( greaterthan + lessthan )
  pval <- c(p_greater,p_less)
  names(pval) = c("pval_greater","pval_less")
  return(pval)
})

permute_res %>% kbl() %>% kable_styling()
SOCS3 POMC_2 TNF NPY_1 NPY_2 LEP
pval_greater 0.5288 0.2046 0.4421 0.9019 0.4853 0.9999
pval_less 0.4712 0.7954 0.5579 0.0981 0.5147 0.0001

Test association of methylation with BMI

Now run a spearman correlation test of BMI with Beta vals.

z <- samplesheet$Del_BMI

genes <- amp

genes %>% kbl() %>% kable_styling()
seqnames start end width strand gene_names
17 78358469 78358619 151
SOCS3
2 25161598 25161833 236
POMC_2
2 25168373 25168611 239
POMC_1
6 31575210 31575467 258
TNF
7 24283548 24283843 296
NPY_1
7 24283796 24283936 141
NPY_2
7 128241036 128241347 312
LEP
par(mfrow=c(1,2))
x <- lapply( 1:nrow(meth), function(i) {
  x <- as.vector(percMethylation(meth)[i,])
  cor <- cor.test(x,z,method="pearson")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

  #plot(z,x,xlab="GWG",ylab="Beta",main="Pearson")
  #mtext(HEADER)
  #mylm <- lm( x ~ z )
  #abline(mylm,lwd=3,lty=2,col="red")

  cor <- cor.test(x,z,method="spearman")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

  plot(rank(z),rank(x),xlab="rank(GWG)",ylab="rank(Beta)",main="Spearman")
  mtext(HEADER)
  mylm <- lm( rank(x) ~ rank(z) )
  abline(mylm,lwd=3,lty=2,col="red")

  c("p"=p,"r"=r)
})
## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

xx <- as.data.frame(t(sapply(x,function(x){ x[c(2,1)] } )))
xx$FDR <- p.adjust(xx[,2],method="fdr")
xx <- data.frame(meth$chr,meth$start,xx)
colnames(xx) <- c("seqname","pos","rho","p","FDR")

gr <- GRanges(seqnames = xx$seqname, ranges = IRanges(xx$pos) )
gr$r <- xx$r
gr$p <- xx$p
gr$FDR <- xx$FDR

ol <- findOverlaps(gr,genes)

# off target gene methylation
ot <- gr[-queryHits(ol)]
ot %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR
16 14989709 14989709 1
-0.0993051 0.6601667 0.9667187
16 14989712 14989712 1
0.0910634 0.6869246 0.9701925
16 14989741 14989741 1
0.0034161 0.9879622 0.9952266
16 14989762 14989762 1
-0.0176139 0.9379875 0.9715310
16 14989764 14989764 1
-0.1921398 0.3916478 0.8506262
16 14989771 14989771 1
-0.0386479 0.8644152 0.9715310
16 14989775 14989775 1
0.0567624 0.8018913 0.9715310
16 14989785 14989785 1
-0.0292328 0.8972490 0.9715310
16 14989801 14989801 1
-0.0205489 0.9276785 0.9715310
16 14989804 14989804 1
0.0528567 0.8152869 0.9715310
16 14989809 14989809 1
0.1132183 0.6159058 0.9440211
16 14989812 14989812 1
0.4730764 0.0261730 0.5122438
16 14989820 14989820 1
0.3332365 0.1296505 0.6819432
16 14989827 14989827 1
0.0144109 0.9492486 0.9715310
16 14989844 14989844 1
-0.0324951 0.8858512 0.9715310
16 14989857 14989857 1
0.2205519 0.3239804 0.8506262
5 865252 865252 1
0.2553673 0.2513792 0.8373424
5 865254 865254 1
0.0141243 0.9502566 0.9715310
5 865278 865278 1
0.0728814 0.7472112 0.9715310
5 865296 865296 1
-0.1841808 0.4119240 0.8506262
5 865349 865349 1
-0.0971752 0.6670450 0.9667187
5 865357 865357 1
-0.3282486 0.1358470 0.6819432
5 865391 865391 1
0.3632769 0.0965542 0.6819432
5 865394 865394 1
0.1559322 0.4883399 0.8919551
5 865435 865435 1
0.5299436 0.0111879 0.3831859
5 865441 865441 1
0.1158192 0.6077672 0.9440211
5 865466 865466 1
-0.3073447 0.1641116 0.6819432
5 865469 865469 1
-0.2344633 0.2935954 0.8506262
5 865473 865473 1
-0.1446328 0.5207567 0.8919551
5 865480 865480 1
0.1146893 0.6112976 0.9440211
5 865483 865483 1
-0.3038270 0.1692414 0.6819432
5 865485 865485 1
0.3211296 0.1450520 0.6819432
5 10649447 10649447 1
0.0961539 0.6703524 0.9667187
5 10649449 10649449 1
-0.0333333 0.8829258 0.9715310
5 10649486 10649486 1
-0.1870057 0.4046626 0.8506262
5 10649495 10649495 1
0.1163842 0.6060052 0.9440211
5 10649503 10649503 1
-0.3293786 0.1344251 0.6819432
5 10649506 10649506 1
-0.2120994 0.3433302 0.8506262
5 10649508 10649508 1
0.1204539 0.5933757 0.9440211
5 131945728 131945728 1
-0.3269463 0.1374990 0.6819432
5 131945736 131945736 1
-0.0653963 0.7724738 0.9715310
5 131945738 131945738 1
-0.0761675 0.7361974 0.9715310
5 131945745 131945745 1
0.2261393 0.3115571 0.8506262
5 131945789 131945789 1
0.3209040 0.1453507 0.6819432
8 22055661 22055661 1
-0.1745763 0.4371388 0.8584949
# on target methylation
gr <- gr[queryHits(ol)]

gr$gene_names <- genes$gene_names[subjectHits(ol) ]

gr %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR gene_names
17 78358500 78358500 1
0.2186441 0.3282893 0.8506262 SOCS3
17 78358506 78358506 1
-0.2016949 0.3680608 0.8506262 SOCS3
17 78358514 78358514 1
0.2039548 0.3626042 0.8506262 SOCS3
17 78358539 78358539 1
0.0327684 0.8848972 0.9715310 SOCS3
17 78358556 78358556 1
0.0152542 0.9462825 0.9715310 SOCS3
17 78358581 78358581 1
0.1740113 0.4386470 0.8584949 SOCS3
17 78358587 78358587 1
-0.1864407 0.4061092 0.8506262 SOCS3
2 25161599 25161599 1
0.1988701 0.3749474 0.8506262 POMC_2
2 25161616 25161616 1
0.2598870 0.2427947 0.8373424 POMC_2
2 25161619 25161619 1
0.5937854 0.0035740 0.3831859 POMC_2
2 25161623 25161623 1
0.5395481 0.0095538 0.3831859 POMC_2
2 25161628 25161628 1
-0.0220339 0.9224668 0.9715310 POMC_2
2 25161637 25161637 1
0.1581921 0.4819795 0.8919551 POMC_2
2 25161653 25161653 1
0.3096046 0.1608736 0.6819432 POMC_2
2 25161661 25161661 1
0.3062147 0.1657475 0.6819432 POMC_2
2 25161671 25161671 1
0.0751413 0.7396317 0.9715310 POMC_2
2 25161686 25161686 1
0.2096046 0.3491689 0.8506262 POMC_2
2 25161689 25161689 1
0.3322034 0.1309170 0.6819432 POMC_2
2 25161699 25161699 1
0.1802260 0.4222086 0.8506262 POMC_2
2 25161716 25161716 1
0.2649718 0.2333672 0.8373424 POMC_2
2 25161720 25161720 1
0.3757063 0.0848641 0.6819432 POMC_2
2 25161728 25161728 1
0.1435028 0.5240536 0.8919551 POMC_2
2 25161742 25161742 1
0.3067797 0.1649281 0.6819432 POMC_2
2 25161764 25161764 1
0.2310735 0.3008311 0.8506262 POMC_2
2 25161766 25161766 1
0.0559322 0.8047342 0.9715310 POMC_2
2 25161785 25161785 1
0.5141244 0.0143733 0.3938289 POMC_2
2 25161792 25161792 1
0.2293786 0.3044896 0.8506262 POMC_2
2 25161799 25161799 1
0.0457627 0.8397430 0.9715310 POMC_2
2 25161804 25161804 1
0.1451978 0.5191119 0.8919551 POMC_2
2 25161811 25161811 1
0.0299435 0.8947641 0.9715310 POMC_2
2 25161813 25161813 1
0.3299449 0.1337165 0.6819432 POMC_2
2 25161817 25161817 1
-0.1007873 0.6553956 0.9667187 POMC_2
2 25161825 25161825 1
0.1660697 0.4601376 0.8755396 POMC_2
6 31575257 31575257 1
-0.0581921 0.7970009 0.9715310 TNF
6 31575316 31575316 1
-0.0197740 0.9303992 0.9715310 TNF
6 31575322 31575322 1
-0.2526137 0.2567035 0.8373424 TNF
6 31575391 31575391 1
-0.1118644 0.6201598 0.9440211 TNF
6 31575397 31575397 1
-0.0305085 0.8927894 0.9715310 TNF
6 31575399 31575399 1
0.0683616 0.7624376 0.9715310 TNF
6 31575414 31575414 1
-0.2548023 0.2524658 0.8373424 TNF
6 31575441 31575441 1
0.0079096 0.9721322 0.9865342 TNF
7 24283574 24283574 1
0.2123457 0.3427568 0.8506262 NPY_1
7 24283578 24283578 1
-0.0807837 0.7208101 0.9715310 NPY_1
7 24283596 24283596 1
-0.0612801 0.7864634 0.9715310 NPY_1
7 24283618 24283618 1
0.3085082 0.1624389 0.6819432 NPY_1
7 24283628 24283628 1
0.1515522 0.5007851 0.8919551 NPY_1
7 24283641 24283641 1
0.1464438 0.5154934 0.8919551 NPY_1
7 24283672 24283672 1
-0.0462217 0.8381560 0.9715310 NPY_1
7 24283696 24283696 1
-0.5348893 0.0103201 0.3831859 NPY_1
7 24283698 24283698 1
-0.0168338 0.9407289 0.9715310 NPY_1
7 24283710 24283710 1
-0.3830089 0.0785078 0.6801308 NPY_1
7 24283713 24283713 1
-0.4038837 0.0623042 0.6801308 NPY_1
7 24283722 24283722 1
-0.0919088 0.6841625 0.9701925 NPY_1
7 24283724 24283724 1
-0.1884163 0.4010633 0.8506262 NPY_1
7 24283731 24283731 1
-0.2098056 0.3486963 0.8506262 NPY_1
7 24283776 24283776 1
-0.1809599 0.4202898 0.8506262 NPY_1
7 24283820 24283820 1
-0.0570622 0.8008653 0.9715310 NPY_1
7 24283820 24283820 1
-0.0570622 0.8008653 0.9715310 NPY_2
7 24283854 24283854 1
-0.2423729 0.2771351 0.8506262 NPY_2
7 24283859 24283859 1
-0.2638419 0.2354412 0.8373424 NPY_2
7 24283894 24283894 1
-0.2796611 0.2074917 0.7896212 NPY_2
7 24283905 24283905 1
0.0288136 0.8987151 0.9715310 NPY_2
7 128241074 128241074 1
-0.2028249 0.3653266 0.8506262 LEP
7 128241076 128241076 1
-0.3519775 0.1081756 0.6819432 LEP
7 128241078 128241078 1
0.0000000 1.0000000 1.0000000 LEP
7 128241090 128241090 1
-0.4079097 0.0594971 0.6801308 LEP
7 128241092 128241092 1
-0.0615819 0.7854355 0.9715310 LEP
7 128241095 128241095 1
-0.2952812 0.1821631 0.7130385 LEP
7 128241108 128241108 1
0.1423729 0.5273603 0.8919551 LEP
7 128241116 128241116 1
-0.0864407 0.7020953 0.9715310 LEP
7 128241118 128241118 1
-0.4022600 0.0634645 0.6801308 LEP
7 128241132 128241132 1
-0.1355932 0.5474044 0.9010509 LEP
7 128241151 128241151 1
-0.1338983 0.5524692 0.9010509 LEP
7 128241155 128241155 1
-0.3949153 0.0689196 0.6801308 LEP
7 128241160 128241160 1
0.0717514 0.7510096 0.9715310 LEP
7 128241163 128241163 1
-0.3819210 0.0794313 0.6801308 LEP
7 128241178 128241178 1
0.0997457 0.6587470 0.9667187 LEP
7 128241183 128241183 1
-0.0299435 0.8947641 0.9715310 LEP
7 128241193 128241193 1
-0.0746606 0.7412417 0.9715310 LEP
7 128241204 128241204 1
-0.3158193 0.1521993 0.6819432 LEP
7 128241207 128241207 1
-0.2229443 0.3186249 0.8506262 LEP
7 128241216 128241216 1
-0.4762713 0.0250416 0.5122438 LEP
7 128241227 128241227 1
-0.2107345 0.3465173 0.8506262 LEP
7 128241240 128241240 1
-0.1666667 0.4585034 0.8755396 LEP
7 128241245 128241245 1
-0.3909605 0.0720002 0.6801308 LEP
7 128241259 128241259 1
-0.4209040 0.0510935 0.6801308 LEP
7 128241277 128241277 1
-0.2429379 0.2759820 0.8506262 LEP
7 128241286 128241286 1
-0.0655367 0.7719978 0.9715310 LEP
7 128241291 128241291 1
-0.1881356 0.4017780 0.8506262 LEP
7 128241297 128241297 1
-0.1382137 0.5396160 0.9010509 LEP
7 128241316 128241316 1
0.0245832 0.9135270 0.9715310 LEP
7 128241319 128241319 1
-0.1497175 0.5060438 0.8919551 LEP
7 128241321 128241321 1
-0.4355933 0.0427307 0.6801308 LEP

Graph of correlation coefficient and p-values across gene loci

xxgr <- GRanges(xx,seqnames=xx$seqname,ranges=IRanges(xx$pos,end=xx$pos),strand="+")

mygenenames <- unique(gr$gene_names)

sapply(mygenenames, function(mygenename) {
  mygene <- gr[gr$gene_names==mygenename,]
  myol <- findOverlaps(xxgr,mygene)
  x <- xxgr[queryHits(myol),]
  par(mfrow=c(2,1))
  par(mar=c(5,4,2,2))
  barplot(-log(x$p),names=x$pos,las=2,cex.names=0.5,ylab="-log(p) nominal",main=mygenename)
  abline(h=-log(0.05))
  barplot(x$rho,names=x$pos,las=2,cex.names=0.5,ylab="Spearman's rho")
})

## $SOCS3
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## [6,]  6.7
## [7,]  7.9
## 
## $POMC_2
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## [17,] 19.9
## [18,] 21.1
## [19,] 22.3
## [20,] 23.5
## [21,] 24.7
## [22,] 25.9
## [23,] 27.1
## [24,] 28.3
## [25,] 29.5
## [26,] 30.7
## 
## $TNF
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## [6,]  6.7
## [7,]  7.9
## [8,]  9.1
## 
## $NPY_1
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## 
## $NPY_2
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## 
## $LEP
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## [17,] 19.9
## [18,] 21.1
## [19,] 22.3
## [20,] 23.5
## [21,] 24.7
## [22,] 25.9
## [23,] 27.1
## [24,] 28.3
## [25,] 29.5
## [26,] 30.7
## [27,] 31.9
## [28,] 33.1
## [29,] 34.3
## [30,] 35.5
## [31,] 36.7

Permutation test

Here I’m going to resample the existing p-value data with random methylation direction.

From that distribution I can estimate the

scores <- -log10(gr$p) * sample(c(-1,1),length(gr$p),replace=TRUE)

npermutes = 10000

permute_res <- sapply(mygenenames, function(mygenename) {
  mygene <- gr[gr$gene_names==mygenename,]
  myol <- findOverlaps(xxgr,mygene)
  x <- xxgr[queryHits(myol),]
  xscore <- mean(-log10(x$p) * as.data.frame(x)[,8])
  permutes <- replicate(n=npermutes ,  mean( -log10(gr$p) * sample(c(-1,1),length(gr$p),replace=TRUE ) ) )
  greaterthan <- length(which(permutes > xscore))
  lessthan <- length(which(permutes < xscore))
  p_greater = greaterthan / ( greaterthan + lessthan )
  p_less = lessthan / ( greaterthan + lessthan )
  pval <- c(p_greater,p_less)
  names(pval) = c("pval_greater","pval_less")
  return(pval)
})

permute_res %>% kbl() %>% kable_styling()
SOCS3 POMC_2 TNF NPY_1 NPY_2 LEP
pval_greater 0.4344 0.0002 0.7028 0.9376 0.9048 0.9964
pval_less 0.5656 0.9998 0.2972 0.0624 0.0952 0.0036

Test association of methylation with maternal age

Now run a spearman correlation test of maternal age with Beta vals.

z <- samplesheet$Age

genes <- amp

genes %>% kbl() %>% kable_styling()
seqnames start end width strand gene_names
17 78358469 78358619 151
SOCS3
2 25161598 25161833 236
POMC_2
2 25168373 25168611 239
POMC_1
6 31575210 31575467 258
TNF
7 24283548 24283843 296
NPY_1
7 24283796 24283936 141
NPY_2
7 128241036 128241347 312
LEP
par(mfrow=c(1,2))
x <- lapply( 1:nrow(meth), function(i) {
  x <- as.vector(percMethylation(meth)[i,])
  cor <- cor.test(x,z,method="pearson")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

  #plot(z,x,xlab="GWG",ylab="Beta",main="Pearson")
  #mtext(HEADER)
  #mylm <- lm( x ~ z )
  #abline(mylm,lwd=3,lty=2,col="red")

  cor <- cor.test(x,z,method="spearman")
  p <- cor$p.value
  r <- cor$estimate
  CHR=as.vector(seqnames(GRanges(meth)))[i]
  POS=as.character(start(ranges(GRanges(meth)))[i])
  CHRPOS=paste("chr",CHR,":",POS,sep="")
  HEADER = paste("Site",i,CHRPOS,"p=",round(p,3)," r=",round(r,3))

  plot(rank(z),rank(x),xlab="rank(GWG)",ylab="rank(Beta)",main="Spearman")
  mtext(HEADER)
  mylm <- lm( rank(x) ~ rank(z) )
  abline(mylm,lwd=3,lty=2,col="red")

  c("p"=p,"r"=r)
})
## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

## Warning in cor.test.default(x, z, method = "spearman"): Cannot compute exact p-
## value with ties

xx <- as.data.frame(t(sapply(x,function(x){ x[c(2,1)] } )))
xx$FDR <- p.adjust(xx[,2],method="fdr")
xx <- data.frame(meth$chr,meth$start,xx)
colnames(xx) <- c("seqname","pos","rho","p","FDR")

gr <- GRanges(seqnames = xx$seqname, ranges = IRanges(xx$pos) )
gr$r <- xx$r
gr$p <- xx$p
gr$FDR <- xx$FDR

ol <- findOverlaps(gr,genes)

# off target gene methylation
ot <- gr[-queryHits(ol)]
ot %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR
16 14989709 14989709 1
-0.1698490 0.4498433 0.8255698
16 14989712 14989712 1
-0.0261366 0.9080847 0.9794662
16 14989741 14989741 1
-0.2367860 0.2887003 0.7031160
16 14989762 14989762 1
-0.0393836 0.8618580 0.9745175
16 14989764 14989764 1
-0.1198022 0.5953905 0.8848622
16 14989771 14989771 1
0.1478733 0.5113567 0.8756983
16 14989775 14989775 1
0.2785964 0.2092996 0.6993671
16 14989785 14989785 1
0.0191896 0.9324517 0.9794662
16 14989801 14989801 1
0.1164006 0.6059540 0.8848622
16 14989804 14989804 1
-0.0319726 0.8876751 0.9745175
16 14989809 14989809 1
-0.3511533 0.1090615 0.6326998
16 14989812 14989812 1
-0.1212101 0.5910412 0.8848622
16 14989820 14989820 1
-0.1279685 0.5703536 0.8848622
16 14989827 14989827 1
0.1098508 0.6265082 0.8848622
16 14989844 14989844 1
-0.0624475 0.7824892 0.9344516
16 14989857 14989857 1
-0.2986565 0.1769814 0.6993671
5 865252 865252 1
0.2565300 0.2491523 0.7031160
5 865254 865254 1
-0.3938757 0.0697195 0.5786634
5 865278 865278 1
-0.3206625 0.1456710 0.6652307
5 865296 865296 1
-0.0192965 0.9320761 0.9794662
5 865349 865349 1
-0.2605028 0.2416401 0.7031160
5 865357 865357 1
-0.0709430 0.7537304 0.9344516
5 865391 865391 1
-0.0039728 0.9860007 0.9860007
5 865394 865394 1
-0.0533492 0.8135950 0.9366598
5 865435 865435 1
0.1668580 0.4579803 0.8255698
5 865441 865441 1
0.3842275 0.0774829 0.5786634
5 865466 865466 1
0.0800237 0.7233363 0.9344516
5 865469 865469 1
-0.2383686 0.2853943 0.7031160
5 865473 865473 1
-0.4506302 0.0353165 0.5786634
5 865480 865480 1
0.2888800 0.1922732 0.6993671
5 865483 865483 1
0.0665568 0.7685418 0.9344516
5 865485 865485 1
-0.0134940 0.9524738 0.9794662
5 10649447 10649447 1
-0.2159108 0.3345222 0.7638257
5 10649449 10649449 1
0.0669702 0.7671423 0.9344516
5 10649486 10649486 1
0.1418861 0.5287880 0.8848622
5 10649495 10649495 1
-0.2491519 0.2634991 0.7031160
5 10649503 10649503 1
-0.4835477 0.0226102 0.5786634
5 10649506 10649506 1
-0.0074498 0.9737516 0.9809116
5 10649508 10649508 1
-0.1210023 0.5916822 0.8848622
5 131945728 131945728 1
-0.2592907 0.2439163 0.7031160
5 131945736 131945736 1
-0.1808520 0.4205717 0.8231188
5 131945738 131945738 1
0.0324606 0.8859714 0.9745175
5 131945745 131945745 1
0.1192923 0.5969693 0.8848622
5 131945789 131945789 1
0.2082888 0.3522715 0.7656209
8 22055661 22055661 1
0.1010229 0.6546384 0.9059137
# on target methylation
gr <- gr[queryHits(ol)]

gr$gene_names <- genes$gene_names[subjectHits(ol) ]

gr %>% kbl() %>% kable_styling()
seqnames start end width strand r p FDR gene_names
17 78358500 78358500 1
-0.2429090 0.2760410 0.7031160 SOCS3
17 78358506 78358506 1
-0.4409819 0.0399460 0.5786634 SOCS3
17 78358514 78358514 1
-0.2582327 0.2459146 0.7031160 SOCS3
17 78358539 78358539 1
-0.3967135 0.0675523 0.5786634 SOCS3
17 78358556 78358556 1
-0.1861545 0.4068431 0.8154197 SOCS3
17 78358581 78358581 1
-0.2797993 0.2072576 0.6993671 SOCS3
17 78358587 78358587 1
-0.3870652 0.0751352 0.5786634 SOCS3
2 25161599 25161599 1
-0.1782089 0.4275072 0.8249082 POMC_2
2 25161616 25161616 1
-0.0539167 0.8116462 0.9366598 POMC_2
2 25161619 25161619 1
-0.0652676 0.7729103 0.9344516 POMC_2
2 25161623 25161623 1
-0.1566422 0.4863371 0.8542075 POMC_2
2 25161628 25161628 1
-0.2440440 0.2737332 0.7031160 POMC_2
2 25161637 25161637 1
-0.2366660 0.2889521 0.7031160 POMC_2
2 25161653 25161653 1
-0.2270177 0.3096308 0.7313694 POMC_2
2 25161661 25161661 1
-0.3314459 0.1318513 0.6420154 POMC_2
2 25161671 25161671 1
-0.4693591 0.0275403 0.5786634 POMC_2
2 25161686 25161686 1
-0.3439318 0.1170512 0.6326998 POMC_2
2 25161689 25161689 1
-0.2951230 0.1824084 0.6993671 POMC_2
2 25161699 25161699 1
-0.2968257 0.1797793 0.6993671 POMC_2
2 25161716 25161716 1
-0.3972810 0.0671251 0.5786634 POMC_2
2 25161720 25161720 1
-0.0964825 0.6692874 0.9169237 POMC_2
2 25161728 25161728 1
-0.1685607 0.4533391 0.8255698 POMC_2
2 25161742 25161742 1
-0.2349633 0.2925373 0.7031160 POMC_2
2 25161764 25161764 1
-0.1333729 0.5540435 0.8848622 POMC_2
2 25161766 25161766 1
-0.4761697 0.0250770 0.5786634 POMC_2
2 25161785 25161785 1
0.0601597 0.7902827 0.9344516 POMC_2
2 25161792 25161792 1
-0.0908071 0.6877627 0.9287511 POMC_2
2 25161799 25161799 1
0.2786642 0.2091841 0.6993671 POMC_2
2 25161804 25161804 1
0.1146439 0.6114394 0.8848622 POMC_2
2 25161811 25161811 1
0.3456345 0.1151304 0.6326998 POMC_2
2 25161813 25161813 1
0.2584951 0.2454179 0.7031160 POMC_2
2 25161817 25161817 1
-0.1398898 0.5346614 0.8848622 POMC_2
2 25161825 25161825 1
0.2375039 0.2871976 0.7031160 POMC_2
6 31575257 31575257 1
-0.0079456 0.9720054 0.9809116 TNF
6 31575316 31575316 1
0.4148749 0.0548705 0.5786634 TNF
6 31575322 31575322 1
0.3999479 0.0651450 0.5786634 TNF
6 31575391 31575391 1
0.1135089 0.6149946 0.8848622 TNF
6 31575397 31575397 1
0.2718537 0.2209940 0.7031160 TNF
6 31575399 31575399 1
0.2065861 0.3563101 0.7656209 TNF
6 31575414 31575414 1
0.4614135 0.0306533 0.5786634 TNF
6 31575441 31575441 1
0.6135154 0.0023924 0.1638798 TNF
7 24283574 24283574 1
0.5441016 0.0088507 0.4041827 NPY_1
7 24283578 24283578 1
0.1530286 0.4965730 0.8611455 NPY_1
7 24283596 24283596 1
0.3282058 0.1359011 0.6420154 NPY_1
7 24283618 24283618 1
0.7986216 0.0000084 0.0011463 NPY_1
7 24283628 24283628 1
0.1669375 0.4577632 0.8255698 NPY_1
7 24283641 24283641 1
0.0447101 0.8433847 0.9628642 NPY_1
7 24283672 24283672 1
-0.1074819 0.6340097 0.8863197 NPY_1
7 24283696 24283696 1
0.1267504 0.5740585 0.8848622 NPY_1
7 24283698 24283698 1
0.1295516 0.5655542 0.8848622 NPY_1
7 24283710 24283710 1
0.1619861 0.4713956 0.8387169 NPY_1
7 24283713 24283713 1
0.0752012 0.7394309 0.9344516 NPY_1
7 24283722 24283722 1
0.3412925 0.1200744 0.6326998 NPY_1
7 24283724 24283724 1
0.3714947 0.0887002 0.5786634 NPY_1
7 24283731 24283731 1
0.0668577 0.7675232 0.9344516 NPY_1
7 24283776 24283776 1
0.2901296 0.1902703 0.6993671 NPY_1
7 24283820 24283820 1
0.2060186 0.3576623 0.7656209 NPY_1
7 24283820 24283820 1
0.2060186 0.3576623 0.7656209 NPY_2
7 24283854 24283854 1
-0.1992080 0.3741196 0.7791827 NPY_2
7 24283859 24283859 1
-0.0647000 0.7748356 0.9344516 NPY_2
7 24283894 24283894 1
-0.1118062 0.6203430 0.8848622 NPY_2
7 24283905 24283905 1
-0.0590246 0.7941566 0.9344516 NPY_2
7 128241074 128241074 1
-0.0578895 0.7980353 0.9344516 LEP
7 128241076 128241076 1
-0.3371213 0.1249668 0.6340906 LEP
7 128241078 128241078 1
-0.0340527 0.8804167 0.9745175 LEP
7 128241090 128241090 1
-0.3853626 0.0765373 0.5786634 LEP
7 128241092 128241092 1
-0.2888800 0.1922732 0.6993671 LEP
7 128241095 128241095 1
-0.3843360 0.0773921 0.5786634 LEP
7 128241108 128241108 1
-0.1867221 0.4053885 0.8154197 LEP
7 128241116 128241116 1
-0.2678809 0.2280827 0.7031160 LEP
7 128241118 128241118 1
-0.1129413 0.6167753 0.8848622 LEP
7 128241132 128241132 1
-0.2474493 0.2668830 0.7031160 LEP
7 128241151 128241151 1
-0.3422292 0.1189951 0.6326998 LEP
7 128241155 128241155 1
-0.3802547 0.0808617 0.5786634 LEP
7 128241160 128241160 1
0.0312149 0.8903212 0.9745175 LEP
7 128241163 128241163 1
-0.3013660 0.1728956 0.6993671 LEP
7 128241178 128241178 1
-0.2091991 0.3501231 0.7656209 LEP
7 128241183 128241183 1
-0.0295123 0.8962716 0.9745175 LEP
7 128241193 128241193 1
-0.1846606 0.4106858 0.8154197 LEP
7 128241204 128241204 1
-0.1271299 0.5729030 0.8848622 LEP
7 128241207 128241207 1
-0.1986966 0.3753727 0.7791827 LEP
7 128241216 128241216 1
-0.2854748 0.1978036 0.6993671 LEP
7 128241227 128241227 1
0.0119184 0.9580180 0.9794662 LEP
7 128241240 128241240 1
0.0896720 0.6914789 0.9287511 LEP
7 128241245 128241245 1
-0.3740117 0.0863924 0.5786634 LEP
7 128241259 128241259 1
0.0130535 0.9540237 0.9794662 LEP
7 128241277 128241277 1
-0.1713984 0.4456584 0.8255698 LEP
7 128241286 128241286 1
0.0726457 0.7480031 0.9344516 LEP
7 128241291 128241291 1
-0.2179370 0.3298950 0.7638257 LEP
7 128241297 128241297 1
-0.0777975 0.7307525 0.9344516 LEP
7 128241316 128241316 1
-0.0218566 0.9230888 0.9794662 LEP
7 128241319 128241319 1
-0.0136211 0.9520269 0.9794662 LEP
7 128241321 128241321 1
-0.0805913 0.7214494 0.9344516 LEP

Graph of correlation coefficient and p-values across gene loci

xxgr <- GRanges(xx,seqnames=xx$seqname,ranges=IRanges(xx$pos,end=xx$pos),strand="+")

mygenenames <- unique(gr$gene_names)

sapply(mygenenames, function(mygenename) {
  mygene <- gr[gr$gene_names==mygenename,]
  myol <- findOverlaps(xxgr,mygene)
  x <- xxgr[queryHits(myol),]
  par(mfrow=c(2,1))
  par(mar=c(5,4,2,2))
  barplot(-log(x$p),names=x$pos,las=2,cex.names=0.5,ylab="-log(p) nominal",main=mygenename)
  abline(h=-log(0.05))
  barplot(x$rho,names=x$pos,las=2,cex.names=0.5,ylab="Spearman's rho")
})

## $SOCS3
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## [6,]  6.7
## [7,]  7.9
## 
## $POMC_2
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## [17,] 19.9
## [18,] 21.1
## [19,] 22.3
## [20,] 23.5
## [21,] 24.7
## [22,] 25.9
## [23,] 27.1
## [24,] 28.3
## [25,] 29.5
## [26,] 30.7
## 
## $TNF
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## [6,]  6.7
## [7,]  7.9
## [8,]  9.1
## 
## $NPY_1
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## 
## $NPY_2
##      [,1]
## [1,]  0.7
## [2,]  1.9
## [3,]  3.1
## [4,]  4.3
## [5,]  5.5
## 
## $LEP
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## [11,] 12.7
## [12,] 13.9
## [13,] 15.1
## [14,] 16.3
## [15,] 17.5
## [16,] 18.7
## [17,] 19.9
## [18,] 21.1
## [19,] 22.3
## [20,] 23.5
## [21,] 24.7
## [22,] 25.9
## [23,] 27.1
## [24,] 28.3
## [25,] 29.5
## [26,] 30.7
## [27,] 31.9
## [28,] 33.1
## [29,] 34.3
## [30,] 35.5
## [31,] 36.7

Permutation test

Here I’m going to resample the existing p-value data with random methylation direction.

From that distribution I can estimate the

scores <- -log10(gr$p) * sample(c(-1,1),length(gr$p),replace=TRUE)

npermutes = 10000

permute_res <- sapply(mygenenames, function(mygenename) {
  mygene <- gr[gr$gene_names==mygenename,]
  myol <- findOverlaps(xxgr,mygene)
  x <- xxgr[queryHits(myol),]
  xscore <- mean(-log10(x$p) * as.data.frame(x)[,8])
  permutes <- replicate(n=npermutes ,  mean( -log10(gr$p) * sample(c(-1,1),length(gr$p),replace=TRUE ) ) )
  greaterthan <- length(which(permutes > xscore))
  lessthan <- length(which(permutes < xscore))
  p_greater = greaterthan / ( greaterthan + lessthan )
  p_less = lessthan / ( greaterthan + lessthan )
  pval <- c(p_greater,p_less)
  names(pval) = c("pval_greater","pval_less")
  return(pval)
})

permute_res %>% kbl() %>% kable_styling()
SOCS3 POMC_2 TNF NPY_1 NPY_2 LEP
pval_greater 0.9997 0.8936 0 0 0.5187 0.9045
pval_less 0.0003 0.1064 1 1 0.4813 0.0955

Session info

sessionInfo()
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] ggbio_1.40.0                           
##  [2] ggplot2_3.3.5                          
##  [3] liftOver_1.16.0                        
##  [4] Homo.sapiens_1.3.1                     
##  [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [6] org.Hs.eg.db_3.13.0                    
##  [7] GO.db_3.13.0                           
##  [8] OrganismDbi_1.34.0                     
##  [9] GenomicFeatures_1.44.2                 
## [10] AnnotationDbi_1.54.1                   
## [11] Biobase_2.52.0                         
## [12] rtracklayer_1.52.1                     
## [13] gwascat_2.24.0                         
## [14] seqinr_4.2-8                           
## [15] gplots_3.1.1                           
## [16] methylKit_1.18.0                       
## [17] limma_3.48.3                           
## [18] GenomicRanges_1.44.0                   
## [19] GenomeInfoDb_1.28.4                    
## [20] IRanges_2.26.0                         
## [21] S4Vectors_0.30.2                       
## [22] BiocGenerics_0.38.0                    
## [23] RColorBrewer_1.1-2                     
## [24] dplyr_1.0.8                            
## [25] kableExtra_1.3.4                       
## [26] reshape2_1.4.4                         
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2                  R.utils_2.11.0             
##   [3] tidyselect_1.1.2            RSQLite_2.2.10             
##   [5] htmlwidgets_1.5.4           grid_4.1.3                 
##   [7] BiocParallel_1.26.2         munsell_0.5.0              
##   [9] withr_2.5.0                 colorspace_2.0-3           
##  [11] filelock_1.0.2              highr_0.9                  
##  [13] knitr_1.37                  rstudioapi_0.13            
##  [15] fastseg_1.38.0              labeling_0.4.2             
##  [17] MatrixGenerics_1.4.3        bbmle_1.0.24               
##  [19] GenomeInfoDbData_1.2.6      farver_2.1.0               
##  [21] bit64_4.0.5                 coda_0.19-4                
##  [23] vctrs_0.3.8                 generics_0.1.2             
##  [25] xfun_0.30                   biovizBase_1.40.0          
##  [27] BiocFileCache_2.0.0         R6_2.5.1                   
##  [29] AnnotationFilter_1.16.0     bitops_1.0-7               
##  [31] cachem_1.0.6                reshape_0.8.8              
##  [33] DelayedArray_0.18.0         assertthat_0.2.1           
##  [35] BiocIO_1.2.0                scales_1.1.1               
##  [37] nnet_7.3-17                 gtable_0.3.0               
##  [39] ensembldb_2.16.4            rlang_1.0.2                
##  [41] systemfonts_1.0.4           splines_4.1.3              
##  [43] lazyeval_0.2.2              dichromat_2.0-0            
##  [45] checkmate_2.0.0             BiocManager_1.30.16        
##  [47] yaml_2.3.5                  snpStats_1.42.0            
##  [49] backports_1.4.1             qvalue_2.24.0              
##  [51] Hmisc_4.6-0                 RBGL_1.68.0                
##  [53] tools_4.1.3                 ellipsis_0.3.2             
##  [55] jquerylib_0.1.4             Rcpp_1.0.8.2               
##  [57] plyr_1.8.6                  base64enc_0.1-3            
##  [59] progress_1.2.2              zlibbioc_1.38.0            
##  [61] purrr_0.3.4                 RCurl_1.98-1.6             
##  [63] prettyunits_1.1.1           rpart_4.1.16               
##  [65] SummarizedExperiment_1.22.0 cluster_2.1.2              
##  [67] magrittr_2.0.2              data.table_1.14.2          
##  [69] mvtnorm_1.1-3               ProtGenerics_1.24.0        
##  [71] matrixStats_0.61.0          hms_1.1.1                  
##  [73] evaluate_0.15               XML_3.99-0.9               
##  [75] emdbook_1.3.12              jpeg_0.1-9                 
##  [77] mclust_5.4.9                gridExtra_2.3              
##  [79] compiler_4.1.3              biomaRt_2.48.3             
##  [81] bdsmatrix_1.3-4             tibble_3.1.6               
##  [83] KernSmooth_2.23-20          crayon_1.5.0               
##  [85] R.oo_1.24.0                 htmltools_0.5.2            
##  [87] mgcv_1.8-39                 tzdb_0.2.0                 
##  [89] Formula_1.2-4               DBI_1.1.2                  
##  [91] dbplyr_2.1.1                MASS_7.3-55                
##  [93] rappdirs_0.3.3              Matrix_1.4-0               
##  [95] ade4_1.7-18                 readr_2.1.2                
##  [97] cli_3.2.0                   R.methodsS3_1.8.1          
##  [99] pkgconfig_2.0.3             GenomicAlignments_1.28.0   
## [101] numDeriv_2016.8-1.1         foreign_0.8-82             
## [103] xml2_1.3.3                  svglite_2.1.0              
## [105] bslib_0.3.1                 webshot_0.5.2              
## [107] XVector_0.32.0              rvest_1.0.2                
## [109] stringr_1.4.0               VariantAnnotation_1.38.0   
## [111] digest_0.6.29               graph_1.70.0               
## [113] Biostrings_2.60.2           rmarkdown_2.13             
## [115] htmlTable_2.4.0             restfulr_0.0.13            
## [117] curl_4.3.2                  Rsamtools_2.8.0            
## [119] gtools_3.9.2                rjson_0.2.21               
## [121] nlme_3.1-155                lifecycle_1.0.1            
## [123] jsonlite_1.8.0              viridisLite_0.4.0          
## [125] BSgenome_1.60.0             fansi_1.0.2                
## [127] pillar_1.7.0                lattice_0.20-45            
## [129] GGally_2.1.2                KEGGREST_1.32.0            
## [131] fastmap_1.1.0               httr_1.4.2                 
## [133] survival_3.3-1              glue_1.6.2                 
## [135] png_0.1-7                   bit_4.0.4                  
## [137] stringi_1.7.6               sass_0.4.0                 
## [139] blob_1.2.2                  latticeExtra_0.6-29        
## [141] caTools_1.18.2              memoise_2.0.1