Project Title: Identification of nuclear modifier gene(s) in consanguineous LHON family NSW08: Analysing vcf files
Isabel Sanchez Lopez, Mark Ziemann and the LHON genetics team
2022-08-16
Intro
Rationale
Leber hereditary optic neuropathy (LHON) is a primary mitochondrial disease characterised by bilateral optic atrophy. LHON is caused by point mutations in mitochondrial DNA (mtDNA) genes encoding subunits of oxidative phosphorylation complex I. Most people with vision loss from LHON harbor one of three primary LHON mutations in MT-ND4 (m.11778G>A), MT-ND6 (m.14484T>C), or MT-ND1 (m.3460G>A). Additional pathogenic variants, including m.14482C>G in MT-ND6, have been identified in multiple LHON pedigrees (Chan C. et al., 1996; Howell N. et al., 1998; Achilli A., et al 2012) and are accepted LHON primary mutations.
The presence of a LHON mutation is not in itself sufficient to cause vision loss. Additional nuclear genetic risk factors are suspected to contribute to disease expression and remain unidentified. Here, we aim to conduct whole exome sequencing (WES) in multiple DNA samples from affected and asymptomatic individuals from the consanguineous LHONNSW08 pedigree to identify nuclear modifier genes in LHON.
Sample selection
The LHONNSW08 pedigree was first described by Howell N. et al., 1998. It is a Turkish pedigree that harbours the m.14482C>G LHON mutation. The pedigree consists of 5 (male) and 2 (female) affected individuals and 17 (male) and 30 (female) asymptomatic carriers. The disease penetrance in this family is 13%, and their mitochondrial haplogroup is I1a (Lopez Sanchez et al., 2020). DNA is available from 6 affected and 28 asymptomatic individuals, from previously extracted blood (Perth), or recently extracted saliva samples (Melbourne). Twenty samples for WES were selected based on affection status and pedigree ascertainment (see Table below).
| Filename | Subject | ID | Diagnosis | Sex |
|---|---|---|---|---|
| 08407_default | IST-08407 | 8-11 | affected | male |
| 08409_default | IST-08409 | 8-13 | unaffected | female |
| 08415_default | IST-08415 | 8-19 | unaffected | female |
| 08416_default | IST-08416 | 8-20 | unaffected | female |
| 08417_default | IST-08417 | 8-21 | unaffected | male |
| 08418_default | IST-08418 | 8-22 | unaffected | female |
| 08420_default | IST-08420 | 8-24 | unaffected | male |
| 08421_default | IST-08421 | 8-25 | unaffected | female |
| 08422_default | IST-8422 | 8-26 | affected | male |
| 08423_default | IST-8423 | 8-27 | unaffected | male |
| 08429_default | IST-8429 | 8-32 | unaffected | male |
| 08431_default | IST-8431 | 8-34 | unaffected | female |
| 08433_default | IST-8433 | 8-36 | affected | male |
| 08435_default | IST-8435 | 8-38 | unaffected | male |
| 08436_default | IST-8436 | 8-39 | unaffected | female |
| 08437_default | IST-8437 | 8-4 | unaffected | female |
| 08440_default | IST-8440 | 8-5 | affected | male |
| 08441_default | IST-8441 | 8-6 | affected | female |
| 08444_default | IST-8444 | 8-9 | unaffected | female |
| SLS_default | - | - | - | - |
Methodology
WES to be performed by AGRF (Australia): WES TWIST Assay, 150bp PE reads NovaSeq 6000 with 10Gb data/sample. Bioinformatics analysis to be conducted by Dr Mark Ziemann (Deakin University).
Load Sample sheet
ss <- read.table("samplesheet.tsv",header=TRUE)
ss## Filename Subject ID Diagnosis Sex
## 1 08407_default IST-08407 8-11 affected male
## 2 08409_default IST-08409 8-13 unaffected female
## 3 08415_default IST-08415 8-19 unaffected female
## 4 08416_default IST-08416 8-20 unaffected female
## 5 08417_default IST-08417 8-21 unaffected male
## 6 08418_default IST-08418 8-22 unaffected female
## 7 08420_default IST-08420 8-24 unaffected male
## 8 08421_default IST-08421 8-25 unaffected female
## 9 08422_default IST-8422 8-26 affected male
## 10 08423_default IST-8423 8-27 unaffected male
## 11 08429_default IST-8429 8-32 unaffected male
## 12 08431_default IST-8431 8-34 unaffected female
## 13 08433_default IST-8433 8-36 affected male
## 14 08435_default IST-8435 8-38 unaffected male
## 15 08436_default IST-8436 8-39 unaffected female
## 16 08437_default IST-8437 8-4 unaffected female
## 17 08440_default IST-8440 8-5 affected male
## 18 08441_default IST-8441 8-6 affected female
## 19 08444_default IST-8444 8-9 unaffected femaleLoading the data
# txdb
txdb <- makeTxDbFromGFF("../../ref/Homo_sapiens.GRCh38.107.gtf.gz")## Import genomic features from the file as a GRanges object ... OK
## Prepare the 'metadata' data frame ... OK
## Make the TxDb object ...## Warning in .get_cds_IDX(mcols0$type, mcols0$phase): The "phase" metadata column contains non-NA values for features of type
## stop_codon. This information was ignored.## OK# load vcf
vcf <- readVcf("merged.vcf", "GRCh38")
# remove refcalls
vcf## class: CollapsedVCF
## dim: 9608936 21
## rowRanges(vcf):
## GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
## info(vcf):
## DataFrame with 4 columns: END, SF, AC, AN
## info(header(vcf)):
## Number Type Description
## END 1 Integer End position (for use with symbolic alleles)
## SF . String Source File (index to sourceFiles, f when filtered)
## AC . Integer Allele count in genotypes
## AN 1 Integer Total number of alleles in called genotypes
## geno(vcf):
## List of length 8: GT, GQ, DP, MIN_DP, AD, VAF, PL, MED_DP
## geno(header(vcf)):
## Number Type Description
## GT 1 String Genotype
## GQ 1 Integer Conditional genotype quality
## DP 1 Integer Read depth
## MIN_DP 1 Integer Minimum DP observed within the GVCF block.
## AD R Integer Read depth for each allele
## VAF A Float Variant allele fractions.
## PL G Integer Phred-scaled genotype likelihoods rounded to the cl...
## MED_DP 1 Integer Median DP observed within the GVCF block rounded to...vcf <- vcf[which(rowRanges(vcf)$FILTER != "RefCall")]
vcf## class: CollapsedVCF
## dim: 2527839 21
## rowRanges(vcf):
## GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
## info(vcf):
## DataFrame with 4 columns: END, SF, AC, AN
## info(header(vcf)):
## Number Type Description
## END 1 Integer End position (for use with symbolic alleles)
## SF . String Source File (index to sourceFiles, f when filtered)
## AC . Integer Allele count in genotypes
## AN 1 Integer Total number of alleles in called genotypes
## geno(vcf):
## List of length 8: GT, GQ, DP, MIN_DP, AD, VAF, PL, MED_DP
## geno(header(vcf)):
## Number Type Description
## GT 1 String Genotype
## GQ 1 Integer Conditional genotype quality
## DP 1 Integer Read depth
## MIN_DP 1 Integer Minimum DP observed within the GVCF block.
## AD R Integer Read depth for each allele
## VAF A Float Variant allele fractions.
## PL G Integer Phred-scaled genotype likelihoods rounded to the cl...
## MED_DP 1 Integer Median DP observed within the GVCF block rounded to...# use only the chromosome sequences in txdb
validseqs <- seqlevels(vcf)[which(seqlevels(vcf) %in% seqlevels(txdb))]
vcf <- vcf[which(seqnames( rowRanges(vcf) ) %in% validseqs)]
seqlevels(vcf) <- as.character(unique(seqnames( rowRanges(vcf) ) ))
seqlevels(vcf) %in% seqlevels(txdb)## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUEvcf## class: CollapsedVCF
## dim: 2522555 21
## rowRanges(vcf):
## GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
## info(vcf):
## DataFrame with 4 columns: END, SF, AC, AN
## info(header(vcf)):
## Number Type Description
## END 1 Integer End position (for use with symbolic alleles)
## SF . String Source File (index to sourceFiles, f when filtered)
## AC . Integer Allele count in genotypes
## AN 1 Integer Total number of alleles in called genotypes
## geno(vcf):
## List of length 8: GT, GQ, DP, MIN_DP, AD, VAF, PL, MED_DP
## geno(header(vcf)):
## Number Type Description
## GT 1 String Genotype
## GQ 1 Integer Conditional genotype quality
## DP 1 Integer Read depth
## MIN_DP 1 Integer Minimum DP observed within the GVCF block.
## AD R Integer Read depth for each allele
## VAF A Float Variant allele fractions.
## PL G Integer Phred-scaled genotype likelihoods rounded to the cl...
## MED_DP 1 Integer Median DP observed within the GVCF block rounded to...table(seqnames(rowRanges(vcf)))##
## 1 10 11 12 13 14 15
## 208092 129509 118568 119880 75601 80292 78928
## 16 17 18 19 2 20 21
## 93210 102144 61626 98891 190390 66487 36909
## 22 3 4 5 6 7 8
## 55079 147895 140036 132733 145280 143284 115744
## 9 MT X Y KI270728.1 KI270727.1 KI270442.1
## 107480 103 67174 2655 282 104 1440
## GL000009.2 GL000205.2 KI270733.1 GL000216.2 KI270744.1 KI270734.1 KI270731.1
## 332 734 206 643 258 55 69
## KI270750.1 KI270721.1 KI270726.1 KI270711.1 KI270713.1
## 142 15 36 93 156barplot(table(seqnames(rowRanges(vcf))))
#coding <- predictCoding(sites, txdb, seqSource = Hsapiens)
Hsapiens <- BSgenome.Hsapiens.UCSC.hg38
seqnames(Hsapiens) <- gsub("chr","",seqnames(Hsapiens))
seqnames(Hsapiens) <- gsub("M","MT",seqnames(Hsapiens))
# fix random contigs
seqnames(Hsapiens)[grep("_",seqnames(Hsapiens))] <-
gsub("v",".",sapply(strsplit( seqnames(Hsapiens)[grep("_",seqnames(Hsapiens))] , "_"),"[[",2))
pred <- unique(predictCoding(vcf, txdb, seqSource=Hsapiens))## Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 1 out-of-bound range located on sequence
## 240434. Note that ranges located on a sequence whose length is unknown
## (NA) or on a circular sequence are not considered out-of-bound (use
## seqlengths() and isCircular() to get the lengths and circularity flags
## of the underlying sequences). You can use trim() to trim these ranges.
## See ?`trim,GenomicRanges-method` for more information.## Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 461500 out-of-bound ranges located on sequences
## 9, 124, 118, 119, 120, 121, 122, 123, 125, 11706, 130, 136, 134, 135,
## 138, 11713, 141, 143, 144, 145, 170, 171, 181, 182, 183, 184, 186,
## 11813, 11816, 11817, 11822, 11824, 11811, 11812, 11829, 11836, 11849,
## 11843, 11844, 11853, 11857, 195, 197, 11864, 11911, 11914, 218, 220,
## 236, 11920, 11921, 244, 251, 265, 11945, 11949, 298, 299, 12000, 12005,
## 12007, 302, 303, 305, 307, 309, 310, 314, 319, 324, 12022, 12024,
## 12025, 12026, 12028, 12029, 12033, 12034, 12054, 364, 368, 12066,
## 12063, 12092, 412, 414, 415, 416, 421, 425, 426, 12117, 12128, 12129,
## 12131, 12135, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 446,
## 12179, 12173, 12174, 12178, 12182, 12183, 12184, 12186, 12187, 12189,
## 12191, 12194, 459, 464, 12207, 12200, 12205, 12204, 12203, 12206, 503,
## 504, 12233, 12234, 12239, 540, 535, 544, 12244, 12241, 12243, 12245,
## 570, 12271, 12272, 12284, 12285, 12302, 12304, 12305, 12306, 12307,
## 12308, 12310, 12311, 12312, 12313, 12314, 12316, 12317, 12315, 590,
## 592, 610, 604, 606, 12340, 12353, 12354, 620, 626, 629, 630, 643, 644,
## 647, 648, 649, 659, 661, 662, 663, 687, 688, 12392, 12393, 12394,
## 12397, 12400, 702, 704, 705, 706, 12437, 716, 715, 724, 726, 728,
## 12468, 12469, 12472, 766, 767, 768, 780, 782, 783, 784, 785, 786, 791,
## 792, 793, 801, 809, 810, 811, 813, 817, 827, 823, 830, 831, 12495,
## 12498, 12505, 12507, 12508, 12513, 12514, 12515, 12519, 12521, 12510,
## 12517, 12522, 12511, 12516, 12512, 12518, 12526, 12533, 12534, 12546,
## 12547, 12548, 12549, 12550, 12565, 12568, 906, 908, 910, 912, 913, 914,
## 915, 920, 921, 923, 924, 925, 12585, 12586, 12589, 12593, 932, 950,
## 951, 953, 992, 1005, 1006, 1010, 1011, 1038, 1040, 1042, 1043, 1044,
## 1046, 12629, 12630, 1047, 1048, 1054, 1055, 1058, 12642, 12643, 12644,
## 1060, 12647, 12648, 1061, 1062, 12649, 12651, 1064, 1065, 1071, 1072,
## 1073, 1079, 1081, 1082, 1086, 1087, 1089, 1091, 1094, 1095, 1110, 1111,
## 1112, 1114, 1113, 1129, 1135, 1136, 1137, 1141, 1144, 12681, 12682,
## 12683, 12684, 12689, 1148, 1166, 1167, 1169, 1174, 1194, 1202, 1205,
## 1207, 1208, 1210, 1211, 1212, 1213, 1214, 1216, 1217, 1223, 12732,
## 12734, 12751, 12752, 12753, 1233, 12756, 12758, 12759, 12760, 12761,
## 12772, 1276, 1277, 1278, 1280, 12814, 12815, 12820, 12821, 12822,
## 12825, 12843, 12846, 1296, 1298, 1299, 1305, 1306, 1310, 1309, 1331,
## 1332, 1333, 12853, 12854, 12855, 12856, 12857, 12863, 12864, 12868,
## 12876, 12867, 12877, 12878, 1336, 12911, 12917, 1345, 12921, 12923,
## 12928, 12929, 1349, 1350, 1359, 1360, 12938, 12946, 12947, 12949,
## 12951, 12953, 12954, 12955, 12956, 1405, 1402, 1404, 1408, 12999,
## 13000, 13001, 13006, 13007, 13027, 13028, 13030, 13031, 13034, 13035,
## 13036, 13038, 13029, 13040, 13043, 13044, 13039, 13053, 13054, 13055,
## 13058, 13059, 1434, 1438, 1432, 1442, 1448, 1446, 1447, 1450, 13070,
## 13071, 13072, 13073, 13075, 13076, 13078, 1455, 1456, 13097, 13100,
## 13110, 1459, 1461, 1466, 1469, 1521, 1520, 1557, 1558, 1559, 1560,
## 1562, 13130, 13162, 13163, 13171, 1632, 1633, 13216, 13217, 13219,
## 13250, 13251, 13253, 1661, 1662, 1663, 1667, 13263, 13257, 13258,
## 13259, 1698, 1699, 1757, 13337, 13338, 13339, 13341, 13342, 13353,
## 13354, 1806, 1808, 1809, 1815, 1817, 1820, 1838, 1839, 1840, 1842,
## 13368, 13370, 13371, 13373, 13375, 13376, 1850, 13384, 13390, 13394,
## 13395, 13396, 13397, 13398, 13401, 1856, 1859, 1860, 1861, 1865, 1866,
## 1874, 1876, 1884, 1887, 1903, 1904, 13415, 13450, 13451, 2028, 2044,
## 2043, 2052, 13489, 13493, 2054, 2055, 2056, 2057, 2059, 2061, 2082,
## 2085, 2088, 2092, 2094, 2095, 2097, 2098, 2099, 2103, 2104, 2105, 2106,
## 2108, 2142, 2143, 2144, 2150, 2152, 13573, 13576, 13583, 13587, 2185,
## 2186, 2187, 2188, 13607, 13615, 13625, 13645, 13659, 13661, 13662,
## 2235, 2236, 2238, 2240, 13668, 13676, 13687, 13693, 13695, 13696,
## 13700, 13705, 2318, 2319, 2320, 2322, 2324, 2325, 2330, 2331, 13754,
## 13755, 13757, 13758, 13759, 13760, 2364, 13854, 2415, 2417, 2424, 2426,
## 2429, 2431, 2432, 13863, 13864, 2437, 2438, 2436, 2434, 13869, 13874,
## 13928, 2509, 2510, 2511, 13945, 13946, 2542, 2564, 14020, 14056, 14057,
## 14059, 14060, 2586, 2590, 2591, 2592, 2595, 2597, 2598, 2600, 14069,
## 14070, 2609, 2610, 2612, 2613, 2616, 2622, 2623, 2624, 2626, 2627,
## 2628, 14097, 14103, 14099, 14100, 14108, 14114, 14115, 14116, 14118,
## 14121, 14122, 14123, 14133, 14134, 2648, 2645, 2652, 14196, 14197,
## 14202, 14208, 14210, 14211, 14212, 14209, 14217, 2724, 2727, 2729,
## 2733, 2739, 2742, 2720, 2721, 2759, 2765, 14343, 14345, 2782, 2783,
## 2787, 2788, 2789, 2790, 14353, 14368, 14369, 2814, 2815, 2818, 2819,
## 2820, 2823, 2824, 2825, 2834, 2848, 2849, 2850, 2858, 2859, 2876, 2872,
## 2873, 2947, 2946, 2954, 14478, 2965, 2966, 2967, 2969, 2971, 2972,
## 2975, 2976, 2977, 2979, 2980, 2981, 2982, 2984, 2986, 2989, 2991, 2995,
## 3001, 3002, 2996, 3010, 3049, 3067, 3072, 3074, 3076, 3079, 3081, 3082,
## 14514, 14518, 14515, 14520, 14523, 3091, 14535, 3097, 3098, 3099, 3110,
## 3111, 3120, 3122, 3131, 3134, 14576, 14577, 3153, 3154, 3155, 3158,
## 3162, 3164, 3177, 3184, 3194, 3219, 3272, 3297, 3316, 14597, 14598,
## 14599, 14600, 14602, 14603, 3354, 3355, 3403, 3414, 3415, 3417, 3421,
## 3422, 14648, 14650, 3456, 3457, 3458, 3463, 3464, 3465, 14682, 14683,
## 14685, 14686, 14720, 14722, 14723, 3506, 3509, 3520, 14751, 14755,
## 14756, 3530, 3534, 3535, 3536, 14776, 14777, 14778, 14781, 14783, 3559,
## 3561, 3563, 3575, 14835, 14839, 3582, 3584, 3607, 3608, 14892, 14893,
## 3611, 3612, 3627, 14941, 14942, 14944, 14946, 14947, 14949, 14945,
## 14951, 14959, 3665, 3666, 3668, 14969, 14970, 14971, 14985, 14982,
## 14984, 14991, 3686, 3688, 3689, 3690, 3691, 3693, 3694, 3696, 3697,
## 3699, 15008, 15009, 3712, 3713, 3714, 15020, 15021, 15024, 15028,
## 15022, 15032, 15040, 15041, 3742, 15056, 15102, 15103, 15108, 15116,
## 3804, 3805, 3809, 3811, 3813, 3814, 3815, 3824, 3825, 3826, 3827, 3829,
## 3830, 3835, 3836, 3831, 3833, 3834, 15153, 15157, 15152, 15156, 3842,
## 3844, 3845, 3847, 3849, 3846, 15161, 15175, 15182, 15188, 15195, 15199,
## 15172, 15177, 15178, 15183, 15189, 15219, 15221, 15231, 15255, 15254,
## 15264, 3908, 3909, 15284, 3919, 3924, 15291, 3942, 3943, 3946, 15311,
## 15362, 3983, 3984, 3985, 3987, 3988, 3989, 15368, 15369, 15370, 15377,
## 15396, 15411, 15417, 15409, 15420, 15421, 4082, 4099, 4101, 4098, 4112,
## 4114, 4145, 4146, 4147, 4148, 4153, 4154, 4155, 4156, 4157, 4165,
## 15544, 15547, 15545, 15546, 4169, 4170, 15556, 15550, 15551, 15552,
## 15555, 15557, 15558, 15573, 15574, 15581, 15569, 15578, 15579, 15650,
## 15651, 15652, 4213, 4218, 4219, 4230, 4229, 15684, 15685, 15686, 15688,
## 15689, 15690, 15692, 15693, 15694, 15695, 15696, 15697, 15701, 15703,
## 15704, 15706, 15699, 15691, 15700, 15711, 4253, 4261, 4262, 4265, 4271,
## 4272, 4273, 4276, 4277, 4290, 4303, 4304, 4294, 4295, 4296, 4297, 4298,
## 4299, 4300, 4301, 4302, 4305, 4306, 4308, 4309, 4311, 4312, 4313, 4314,
## 4315, 4316, 4317, 4318, 4319, 4320, 4321, 4322, 4323, 4324, 4325, 4326,
## 4328, 4329, 4330, 4331, 4332, 4333, 15752, 15763, 15764, 15765, 15770,
## 4366, 4368, 4370, 4371, 4372, 4373, 4374, 4375, 4376, 4377, 4378, 4379,
## 4380, 4381, 4382, 4383, 4384, 4385, 4386, 4387, 4388, 4389, 4390, 4391,
## 4392, 4393, 4394, 4395, 4396, 4398, 4399, 4401, 4402, 4409, 4413,
## 15812, 15813, 4462, 4463, 4464, 4466, 15856, 15879, 15880, 4597, 4598,
## 4600, 4602, 4603, 4604, 4605, 4606, 4608, 4609, 4610, 4611, 4612,
## 15890, 15892, 15894, 15895, 15897, 15898, 15900, 15901, 4634, 15908,
## 15907, 4680, 4651, 4656, 4669, 4681, 4686, 4693, 4707, 4747, 4754,
## 4755, 15918, 15921, 15936, 15937, 15938, 15939, 15942, 15949, 4782,
## 4793, 4794, 4795, 4796, 4864, 4865, 4866, 4867, 4868, 4869, 4876, 4880,
## 4882, 4883, 4884, 4885, 4888, 4889, 4894, 4896, 4903, 16039, 16041,
## 4938, 4939, 4941, 4942, 4944, 4945, 4950, 4951, 4958, 4959, 16075,
## 16078, 4969, 4970, 4972, 16108, 16109, 16115, 16124, 16127, 16125,
## 16126, 16129, 16136, 16147, 16141, 16160, 4995, 5013, 5037, 5038, 5039,
## 16202, 16210, 16218, 16219, 16239, 16240, 16246, 5051, 5063, 5076,
## 5079, 16312, 16314, 16324, 16325, 16329, 16330, 16331, 16334, 16335,
## 16336, 163## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[16020]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[35651]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[39944]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[40219]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[44702]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[46202]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[57589]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[74954]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[76810]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[86863]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[88635]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[94474]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[103931]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[107673]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[113203]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[125039]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[132393]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[139357]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[143259]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[149851]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[150274]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[158991]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[163570]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[163737]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[163796]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[166363]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[168595]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[16020]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[35651]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[39944]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[40219]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[44702]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[46202]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[57589]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[74954]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[76810]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[86863]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[88635]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[94474]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[103931]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[107673]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[113203]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[125039]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[132393]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[139357]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[143259]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[149851]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[150274]]': last base was ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[158991]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[163570]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[163737]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[163796]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[166363]]': last 2 bases were ignored## Warning in .Call2("DNAStringSet_translate", x, skip_code,
## dna_codes[codon_alphabet], : in 'x[[168595]]': last 2 bases were ignoredpred## GRanges object with 54112 ranges and 17 metadata columns:
## seqnames ranges strand | paramRangeID
## <Rle> <IRanges> <Rle> | <factor>
## 1:69270_A/G 1 69270 + | NA
## 1:69511_A/G 1 69511 + | NA
## 1:69897_T/C 1 69897 + | NA
## 1:924533_A/G 1 924533 + | NA
## 1:942451_T/C 1 942451 + | NA
## ... ... ... ... . ...
## KI270711.1:29295_G/T KI270711.1 29295 - | NA
## KI270711.1:29435_G/A KI270711.1 29435 - | NA
## KI270713.1:32011_A/G KI270713.1 32011 - | NA
## KI270713.1:32102_C/G KI270713.1 32102 - | NA
## KI270713.1:32134_A/C KI270713.1 32134 - | NA
## REF ALT QUAL FILTER
## <DNAStringSet> <DNAStringSetList> <numeric> <character>
## 1:69270_A/G A G 28.03 PASS
## 1:69511_A/G A G 35.31 PASS
## 1:69897_T/C T C 14.80 PASS
## 1:924533_A/G A G 26.65 PASS
## 1:942451_T/C T C 36.91 PASS
## ... ... ... ... ...
## KI270711.1:29295_G/T G T 18.40 PASS
## KI270711.1:29435_G/A G A 12.98 PASS
## KI270713.1:32011_A/G A G 24.53 PASS
## KI270713.1:32102_C/G C G 27.47 PASS
## KI270713.1:32134_A/C A C 14.67 PASS
## varAllele CDSLOC PROTEINLOC QUERYID
## <DNAStringSet> <IRanges> <IntegerList> <integer>
## 1:69270_A/G G 243 81 23
## 1:69511_A/G G 484 162 24
## 1:69897_T/C C 870 290 25
## 1:924533_A/G G 102 34 368
## 1:942451_T/C C 1516 506 426
## ... ... ... ... ...
## KI270711.1:29295_G/T A 159 53 2522392
## KI270711.1:29435_G/A T 19 7 2522393
## KI270713.1:32011_A/G C 362 121 2522528
## KI270713.1:32102_C/G C 271 91 2522529
## KI270713.1:32134_A/C G 239 80 2522530
## TXID CDSID GENEID CONSEQUENCE
## <character> <IntegerList> <character> <factor>
## 1:69270_A/G 9 2 ENSG00000186092 synonymous
## 1:69511_A/G 9 2 ENSG00000186092 nonsynonymous
## 1:69897_T/C 9 2 ENSG00000186092 synonymous
## 1:924533_A/G 115 3 ENSG00000187634 synonymous
## 1:942451_T/C 115 18 ENSG00000187634 nonsynonymous
## ... ... ... ... ...
## KI270711.1:29295_G/T 251083 277458 ENSG00000271254 nonsynonymous
## KI270711.1:29435_G/A 251083 277458 ENSG00000271254 nonsynonymous
## KI270713.1:32011_A/G 251087 277460 ENSG00000277475 nonsynonymous
## KI270713.1:32102_C/G 251087 277460 ENSG00000277475 nonsynonymous
## KI270713.1:32134_A/C 251087 277460 ENSG00000277475 nonsense
## REFCODON VARCODON REFAA
## <DNAStringSet> <DNAStringSet> <AAStringSet>
## 1:69270_A/G TCA TCG S
## 1:69511_A/G ACA GCA T
## 1:69897_T/C TCT TCC S
## 1:924533_A/G CCA CCG P
## 1:942451_T/C TGG CGG W
## ... ... ... ...
## KI270711.1:29295_G/T AAC AAA N
## KI270711.1:29435_G/A CCT TCT P
## KI270713.1:32011_A/G ATC ACC I
## KI270713.1:32102_C/G GGG CGG G
## KI270713.1:32134_A/C TTA TGA L
## VARAA
## <AAStringSet>
## 1:69270_A/G S
## 1:69511_A/G A
## 1:69897_T/C S
## 1:924533_A/G P
## 1:942451_T/C R
## ... ...
## KI270711.1:29295_G/T K
## KI270711.1:29435_G/A S
## KI270713.1:32011_A/G T
## KI270713.1:32102_C/G R
## KI270713.1:32134_A/C *
## -------
## seqinfo: 40 sequences from GRCh38 genomeVariant summary data.
table(pred$CONSEQUENCE)##
## frameshift nonsense nonsynonymous synonymous
## 755 373 27531 25453pred2 <- pred[pred$CONSEQUENCE != "synonymous"]Show mito mutations
#mito <- vcf[which(seqnames(vcf) == "MT")]
mito <- vcf[which(rownames(vcf) %in% rownames(mito) )]
mito_rr <- as.data.frame(rowRanges(mito))
mito_geno <- as.data.frame(geno(mito)$GT)
mito_df <- cbind(mito_rr, mito_geno)
write.table(mito_df,file="mito_df.tsv", sep="\t")
mito_df## seqnames start end width strand paramRangeID REF
## MT:150_C/T MT 150 150 1 * <NA> C
## MT:204_T/C MT 204 204 1 * <NA> T
## MT:250_T/C MT 250 250 1 * <NA> T
## MT:263_A/G MT 263 263 1 * <NA> A
## MT:451_A/AT MT 451 451 1 * <NA> A
## MT:499_G/A MT 499 499 1 * <NA> G
## MT:750_A/G MT 750 750 1 * <NA> A
## MT:827_A/G MT 827 827 1 * <NA> A
## MT:1189_T/C MT 1189 1189 1 * <NA> T
## MT:1403_A/G MT 1403 1403 1 * <NA> A
## MT:1411_G/T MT 1411 1411 1 * <NA> G
## MT:1438_A/G MT 1438 1438 1 * <NA> A
## MT:1531_C/T MT 1531 1531 1 * <NA> C
## MT:1537_C/T MT 1537 1537 1 * <NA> C
## MT:1608_GTA/G MT 1608 1610 3 * <NA> GTA
## MT:1625_A/G MT 1625 1625 1 * <NA> A
## MT:1694_T/C MT 1694 1694 1 * <NA> T
## MT:1750_GAT/G MT 1750 1752 3 * <NA> GAT
## MT:1842_A/G MT 1842 1842 1 * <NA> A
## MT:1888_G/A MT 1888 1888 1 * <NA> G
## MT:2617_A/G MT 2617 2617 1 * <NA> A
## MT:2706_A/G MT 2706 2706 1 * <NA> A
## MT:3173_G/A MT 3173 3173 1 * <NA> G
## MT:3547_A/G MT 3547 3547 1 * <NA> A
## MT:3666_G/A MT 3666 3666 1 * <NA> G
## MT:4057_T/C MT 4057 4057 1 * <NA> T
## MT:4240_T/C MT 4240 4240 1 * <NA> T
## MT:4360_G/A MT 4360 4360 1 * <NA> G
## MT:4769_A/G MT 4769 4769 1 * <NA> A
## MT:4820_G/A MT 4820 4820 1 * <NA> G
## MT:4917_A/G MT 4917 4917 1 * <NA> A
## MT:4977_T/C MT 4977 4977 1 * <NA> T
## MT:5152_T/C MT 5152 5152 1 * <NA> T
## MT:6261_G/A MT 6261 6261 1 * <NA> G
## MT:6450_CT/C MT 6450 6451 2 * <NA> CT
## MT:6473_C/T MT 6473 6473 1 * <NA> C
## MT:6646_T/C MT 6646 6646 1 * <NA> T
## MT:7028_C/T MT 7028 7028 1 * <NA> C
## MT:7223_C/T MT 7223 7223 1 * <NA> C
## MT:7241_A/G MT 7241 7241 1 * <NA> A
## MT:8014_A/T MT 8014 8014 1 * <NA> A
## MT:8027_G/A MT 8027 8027 1 * <NA> G
## MT:8269_G/A MT 8269 8269 1 * <NA> G
## MT:8270_CACCCCCTCT/C MT 8270 8279 10 * <NA> CACCCCCTCT
## MT:8271_A/ACCCC MT 8271 8271 1 * <NA> A
## MT:8277_T/C MT 8277 8277 1 * <NA> T
## MT:8455_C/T MT 8455 8455 1 * <NA> C
## MT:8468_C/T MT 8468 8468 1 * <NA> C
## MT:8697_G/A MT 8697 8697 1 * <NA> G
## MT:8702_C/T MT 8702 8702 1 * <NA> C
## MT:8794_C/T MT 8794 8794 1 * <NA> C
## MT:8860_A/G MT 8860 8860 1 * <NA> A
## MT:9156_A/G MT 9156 9156 1 * <NA> A
## MT:9950_T/C MT 9950 9950 1 * <NA> T
## MT:9966_G/A MT 9966 9966 1 * <NA> G
## MT:9983_A/C MT 9983 9983 1 * <NA> A
## MT:10034_T/C MT 10034 10034 1 * <NA> T
## MT:10463_T/C MT 10463 10463 1 * <NA> T
## MT:10685_G/A MT 10685 10685 1 * <NA> G
## MT:10822_C/T MT 10822 10822 1 * <NA> C
## MT:11251_A/G MT 11251 11251 1 * <NA> A
## MT:11425_A/G MT 11425 11425 1 * <NA> A
## MT:11467_A/G MT 11467 11467 1 * <NA> A
## MT:11485_T/C MT 11485 11485 1 * <NA> T
## MT:11719_G/A MT 11719 11719 1 * <NA> G
## MT:11812_A/G MT 11812 11812 1 * <NA> A
## MT:12239_C/T MT 12239 12239 1 * <NA> C
## MT:12244_G/C MT 12244 12244 1 * <NA> G
## MT:12360_C/T MT 12360 12360 1 * <NA> C
## MT:12705_C/T MT 12705 12705 1 * <NA> C
## MT:12940_G/A MT 12940 12940 1 * <NA> G
## MT:13368_G/A MT 13368 13368 1 * <NA> G
## MT:13973_A/T MT 13973 13973 1 * <NA> A
## MT:14233_A/G MT 14233 14233 1 * <NA> A
## MT:14577_T/C MT 14577 14577 1 * <NA> T
## MT:14755_A/G MT 14755 14755 1 * <NA> A
## MT:14757_T/C MT 14757 14757 1 * <NA> T
## MT:14766_C/T MT 14766 14766 1 * <NA> C
## MT:14798_T/C MT 14798 14798 1 * <NA> T
## MT:14905_G/A MT 14905 14905 1 * <NA> G
## MT:15043_G/A MT 15043 15043 1 * <NA> G
## MT:15218_A/G MT 15218 15218 1 * <NA> A
## MT:15301_G/A MT 15301 15301 1 * <NA> G
## MT:15323_G/A MT 15323 15323 1 * <NA> G
## MT:15326_A/G MT 15326 15326 1 * <NA> A
## MT:15597_T/G MT 15597 15597 1 * <NA> T
## MT:15607_A/G MT 15607 15607 1 * <NA> A
## MT:15706_A/G MT 15706 15706 1 * <NA> A
## MT:15884_G/A MT 15884 15884 1 * <NA> G
## MT:15928_G/A MT 15928 15928 1 * <NA> G
## MT:15936_A/G MT 15936 15936 1 * <NA> A
## MT:16067_C/T MT 16067 16067 1 * <NA> C
## MT:16126_T/C MT 16126 16126 1 * <NA> T
## MT:16129_G/A MT 16129 16129 1 * <NA> G
## MT:16179_C/T MT 16179 16179 1 * <NA> C
## MT:16217_T/C MT 16217 16217 1 * <NA> T
## MT:16223_C/T MT 16223 16223 1 * <NA> C
## MT:16224_T/C MT 16224 16224 1 * <NA> T
## MT:16291_C/T MT 16291 16291 1 * <NA> C
## MT:16292_C/T MT 16292 16292 1 * <NA> C
## MT:16294_C/T MT 16294 16294 1 * <NA> C
## MT:16295_C/T MT 16295 16295 1 * <NA> C
## MT:16319_G/A MT 16319 16319 1 * <NA> G
## ALT QUAL FILTER default 08407_default 08409_default
## MT:150_C/T T 41.50 PASS . . .
## MT:204_T/C C 32.27 PASS 0/1 . 0/1
## MT:250_T/C C 31.24 PASS 0/1 . 0/1
## MT:263_A/G G 39.53 PASS 1/1 1/1 1/1
## MT:451_A/AT AT 32.72 PASS 0/1 . 1/1
## MT:499_G/A A 33.10 PASS . . .
## MT:750_A/G G 39.28 PASS 1/1 1/1 1/1
## MT:827_A/G G 40.30 PASS . . .
## MT:1189_T/C C 3.20 PASS . . .
## MT:1403_A/G G 14.80 PASS . . .
## MT:1411_G/T T 15.60 PASS . . .
## MT:1438_A/G G 42.16 PASS 1/1 1/1 1/1
## MT:1531_C/T T 32.60 PASS 0/1 . .
## MT:1537_C/T T 5.60 PASS . . .
## MT:1608_GTA/G G 11.65 PASS . 0/1 .
## MT:1625_A/G G 6.10 PASS . . 0/1
## MT:1694_T/C C 44.60 PASS . . .
## MT:1750_GAT/G G 5.20 PASS . . .
## MT:1842_A/G G 23.90 PASS . . .
## MT:1888_G/A A 21.50 PASS . . .
## MT:2617_A/G G, T 44.39 PASS 0/1 1/2 1/2
## MT:2706_A/G G 32.80 PASS 0/1 1/1 1/1
## MT:3173_G/A A 19.50 PASS . . 1/1
## MT:3547_A/G G 44.80 PASS . . .
## MT:3666_G/A A 32.00 PASS . . .
## MT:4057_T/C C 7.90 PASS . . 0/1
## MT:4240_T/C C 10.40 PASS . . .
## MT:4360_G/A A 18.30 PASS . . .
## MT:4769_A/G G 33.87 PASS 1/1 1/1 1/1
## MT:4820_G/A A 30.80 PASS . . .
## MT:4917_A/G G 40.60 PASS . . .
## MT:4977_T/C C 16.20 PASS . . .
## MT:5152_T/C C 6.70 PASS . . .
## MT:6261_G/A A 46.70 PASS . . .
## MT:6450_CT/C C 4.30 PASS . . .
## MT:6473_C/T T 43.70 PASS . . .
## MT:6646_T/C C 3.80 PASS . . .
## MT:7028_C/T T 36.11 PASS 0/1 0/1 0/1
## MT:7223_C/T T 5.80 PASS . . .
## MT:7241_A/G G 34.10 PASS . . .
## MT:8014_A/T T 43.30 PASS . . .
## MT:8027_G/A A 10.50 PASS . . .
## MT:8269_G/A A 3.70 PASS . . .
## MT:8270_CACCCCCTCT/C C 36.40 PASS . . .
## MT:8271_A/ACCCC ACCCC 13.00 PASS . . .
## MT:8277_T/C C 19.80 PASS . . .
## MT:8455_C/T T 44.60 PASS . . .
## MT:8468_C/T T 9.80 PASS . 0/1 .
## MT:8697_G/A A 33.90 PASS . . .
## MT:8702_C/T T 35.80 PASS . . .
## MT:8794_C/T T 11.17 PASS 0/1 . .
## MT:8860_A/G G 41.22 PASS 1/1 1/1 1/1
## MT:9156_A/G G 10.80 PASS . . .
## MT:9950_T/C C 43.20 PASS . . .
## MT:9966_G/A A 38.93 PASS 0/1 . .
## MT:9983_A/C C 8.90 PASS . . .
## MT:10034_T/C C 39.81 PASS 0/1 . .
## MT:10463_T/C C 45.20 PASS . . .
## MT:10685_G/A A 14.60 PASS . . .
## MT:10822_C/T T 42.60 PASS . . .
## MT:11251_A/G G 42.70 PASS . . .
## MT:11425_A/G G 46.70 PASS . . .
## MT:11467_A/G G 34.88 PASS 0/1 . 0/1
## MT:11485_T/C C 31.35 PASS 0/1 . 0/1
## MT:11719_G/A A 34.24 PASS 0/1 0/1 0/1
## MT:11812_A/G G 41.70 PASS . . .
## MT:12239_C/T T 4.40 PASS . . .
## MT:12244_G/C C 5.90 PASS . . .
## MT:12360_C/T T 41.40 PASS . . .
## MT:12705_C/T T 35.15 PASS 0/1 0/1 0/1
## MT:12940_G/A A 12.90 PASS . . .
## MT:13368_G/A A 43.10 PASS . . .
## MT:13973_A/T T 41.00 PASS . . .
## MT:14233_A/G G 33.30 PASS . . .
## MT:14577_T/C C 23.90 PASS . . .
## MT:14755_A/G G 19.70 PASS . . .
## MT:14757_T/C C 32.10 PASS . . .
## MT:14766_C/T T 32.28 PASS 0/1 0/1 1/1
## MT:14798_T/C C 12.40 PASS . . .
## MT:14905_G/A A 41.10 PASS . . .
## MT:15043_G/A A 45.07 PASS 0/1 0/1 0/1
## MT:15218_A/G G 35.30 PASS . . .
## MT:15301_G/A A 20.71 PASS . 0/1 0/1
## MT:15323_G/A A 14.40 PASS . 0/1 .
## MT:15326_A/G G 41.49 PASS 1/1 1/1 1/1
## MT:15597_T/G G 8.80 PASS . . .
## MT:15607_A/G G 39.20 PASS . . .
## MT:15706_A/G G 36.60 PASS . . .
## MT:15884_G/A A 8.80 PASS . . .
## MT:15928_G/A A 39.80 PASS . . .
## MT:15936_A/G G 21.00 PASS . . .
## MT:16067_C/T T 39.90 PASS . . .
## MT:16126_T/C C 46.40 PASS . . .
## MT:16129_G/A A 30.33 PASS 0/1 1/1 0/1
## MT:16179_C/T T 33.70 PASS . . .
## MT:16217_T/C C 5.60 PASS . . .
## MT:16223_C/T T 32.45 PASS 1/1 . 0/1
## MT:16224_T/C C 8.00 PASS . . .
## MT:16291_C/T T 28.20 PASS . . .
## MT:16292_C/T T 23.40 PASS . . .
## MT:16294_C/T T 15.40 PASS . . .
## MT:16295_C/T T 6.80 PASS . . .
## MT:16319_G/A A 11.30 PASS . . .
## 08415_default 08416_default 08417_default 08418_default
## MT:150_C/T . . . .
## MT:204_T/C 0/1 1/1 0/1 0/1
## MT:250_T/C 0/1 1/1 0/1 0/1
## MT:263_A/G 1/1 1/1 1/1 1/1
## MT:451_A/AT 1/1 1/1 1/1 1/1
## MT:499_G/A . . . .
## MT:750_A/G 1/1 1/1 1/1 1/1
## MT:827_A/G . . . .
## MT:1189_T/C . . . .
## MT:1403_A/G . . . .
## MT:1411_G/T . . . .
## MT:1438_A/G 1/1 1/1 1/1 1/1
## MT:1531_C/T 0/1 1/1 0/1 0/1
## MT:1537_C/T . . . .
## MT:1608_GTA/G . . . .
## MT:1625_A/G . . . .
## MT:1694_T/C . . . .
## MT:1750_GAT/G . . . .
## MT:1842_A/G . . . .
## MT:1888_G/A . . . .
## MT:2617_A/G 1/2 0/2 0/1 0/2
## MT:2706_A/G 0/1 1/1 0/1 0/1
## MT:3173_G/A . . . .
## MT:3547_A/G . . . .
## MT:3666_G/A . . . .
## MT:4057_T/C . . . .
## MT:4240_T/C . . . .
## MT:4360_G/A . . . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4820_G/A . . . .
## MT:4917_A/G . . . .
## MT:4977_T/C . . . .
## MT:5152_T/C . . . .
## MT:6261_G/A . . . .
## MT:6450_CT/C . . . .
## MT:6473_C/T . . . .
## MT:6646_T/C . . . .
## MT:7028_C/T 0/1 0/1 0/1 1/1
## MT:7223_C/T . . . .
## MT:7241_A/G . . . .
## MT:8014_A/T . . . .
## MT:8027_G/A . . . .
## MT:8269_G/A . . . .
## MT:8270_CACCCCCTCT/C . . . .
## MT:8271_A/ACCCC . . . .
## MT:8277_T/C . . . .
## MT:8455_C/T . . . .
## MT:8468_C/T . . . .
## MT:8697_G/A . . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . . .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9156_A/G . . . .
## MT:9950_T/C . . . .
## MT:9966_G/A 0/1 0/1 0/1 0/1
## MT:9983_A/C . . . .
## MT:10034_T/C 0/1 0/1 . 0/1
## MT:10463_T/C . . . .
## MT:10685_G/A . . . .
## MT:10822_C/T . . . .
## MT:11251_A/G . . . .
## MT:11425_A/G . . . .
## MT:11467_A/G . 0/1 . .
## MT:11485_T/C . 0/1 . .
## MT:11719_G/A 0/1 1/1 0/1 0/1
## MT:11812_A/G . . . .
## MT:12239_C/T . . . .
## MT:12244_G/C . . . .
## MT:12360_C/T . . . .
## MT:12705_C/T 0/1 0/1 0/1 0/1
## MT:12940_G/A . . . .
## MT:13368_G/A . . . .
## MT:13973_A/T . . . .
## MT:14233_A/G . . . .
## MT:14577_T/C . . . .
## MT:14755_A/G . . . .
## MT:14757_T/C . . . .
## MT:14766_C/T 1/1 0/1 0/1 1/1
## MT:14798_T/C . . . .
## MT:14905_G/A . . . .
## MT:15043_G/A 0/1 0/1 0/1 0/1
## MT:15218_A/G . . . .
## MT:15301_G/A . . 0/1 .
## MT:15323_G/A . . . .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . .
## MT:15607_A/G . . . .
## MT:15706_A/G . . . .
## MT:15884_G/A . . . .
## MT:15928_G/A . . . .
## MT:15936_A/G . . . .
## MT:16067_C/T . . . .
## MT:16126_T/C . . . .
## MT:16129_G/A 0/1 0/1 0/1 1/1
## MT:16179_C/T . . . .
## MT:16217_T/C . . . .
## MT:16223_C/T 1/1 1/1 0/1 0/1
## MT:16224_T/C . . . .
## MT:16291_C/T . . . .
## MT:16292_C/T . . . .
## MT:16294_C/T . . . .
## MT:16295_C/T . . . .
## MT:16319_G/A . . . .
## 08420_default 08421_default 08422_default 08423_default
## MT:150_C/T . . . .
## MT:204_T/C 0/1 0/1 0/1 0/1
## MT:250_T/C 0/1 0/1 0/1 0/1
## MT:263_A/G 1/1 1/1 1/1 1/1
## MT:451_A/AT 1/1 1/1 1/1 1/1
## MT:499_G/A . . . .
## MT:750_A/G 1/1 1/1 1/1 1/1
## MT:827_A/G . . . .
## MT:1189_T/C . . . .
## MT:1403_A/G . . . .
## MT:1411_G/T . . . .
## MT:1438_A/G 1/1 1/1 1/1 1/1
## MT:1531_C/T 0/1 0/1 0/1 0/1
## MT:1537_C/T . . . .
## MT:1608_GTA/G . 0/1 . .
## MT:1625_A/G . . . .
## MT:1694_T/C . . . .
## MT:1750_GAT/G . . . .
## MT:1842_A/G . . . .
## MT:1888_G/A . . . .
## MT:2617_A/G 0/1 1/2 0/1 0/2
## MT:2706_A/G 0/1 1/1 1/1 1/1
## MT:3173_G/A . . . .
## MT:3547_A/G . . . .
## MT:3666_G/A . . . .
## MT:4057_T/C . . . .
## MT:4240_T/C . 0/1 . .
## MT:4360_G/A . . . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4820_G/A . . . .
## MT:4917_A/G . . . .
## MT:4977_T/C . . . .
## MT:5152_T/C 0/1 . . .
## MT:6261_G/A . . . .
## MT:6450_CT/C . . . .
## MT:6473_C/T . . . .
## MT:6646_T/C . . . .
## MT:7028_C/T 0/1 0/1 0/1 0/1
## MT:7223_C/T . . . .
## MT:7241_A/G . . . .
## MT:8014_A/T . . . .
## MT:8027_G/A . . . .
## MT:8269_G/A . . . .
## MT:8270_CACCCCCTCT/C . . . .
## MT:8271_A/ACCCC . . . .
## MT:8277_T/C . . . .
## MT:8455_C/T . . . .
## MT:8468_C/T . . . 0/1
## MT:8697_G/A . . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . . .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9156_A/G . . . .
## MT:9950_T/C . . . .
## MT:9966_G/A 0/1 0/1 0/1 0/1
## MT:9983_A/C . . . .
## MT:10034_T/C 0/1 1/1 0/1 0/1
## MT:10463_T/C . . . .
## MT:10685_G/A . . . .
## MT:10822_C/T . . . .
## MT:11251_A/G . . . .
## MT:11425_A/G . . . .
## MT:11467_A/G 0/1 . . .
## MT:11485_T/C 0/1 . . .
## MT:11719_G/A 0/1 1/1 0/1 1/1
## MT:11812_A/G . . . .
## MT:12239_C/T . 0/1 . .
## MT:12244_G/C . . . .
## MT:12360_C/T . . . .
## MT:12705_C/T 0/1 0/1 0/1 0/1
## MT:12940_G/A . . . .
## MT:13368_G/A . . . .
## MT:13973_A/T . . . .
## MT:14233_A/G . . . .
## MT:14577_T/C . . . .
## MT:14755_A/G . . . .
## MT:14757_T/C . . . .
## MT:14766_C/T 0/1 0/1 1/1 1/1
## MT:14798_T/C . . . .
## MT:14905_G/A . . . .
## MT:15043_G/A 0/1 0/1 0/1 0/1
## MT:15218_A/G . . . .
## MT:15301_G/A 0/1 0/1 0/1 0/1
## MT:15323_G/A . . . .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . .
## MT:15607_A/G . . . .
## MT:15706_A/G . . . .
## MT:15884_G/A . . . 0/1
## MT:15928_G/A . . . .
## MT:15936_A/G . . . .
## MT:16067_C/T . . . .
## MT:16126_T/C . . . .
## MT:16129_G/A 1/1 0/1 0/1 1/1
## MT:16179_C/T . . . .
## MT:16217_T/C . . . .
## MT:16223_C/T 1/1 0/1 1/1 1/1
## MT:16224_T/C . . . .
## MT:16291_C/T . . . .
## MT:16292_C/T . . . .
## MT:16294_C/T . . . .
## MT:16295_C/T . . 0/1 .
## MT:16319_G/A . . . .
## 08429_default 08431_default 08433_default 08435_default
## MT:150_C/T . . . 0/1
## MT:204_T/C . 0/1 0/1 .
## MT:250_T/C . 0/1 0/1 .
## MT:263_A/G 1/1 1/1 1/1 1/1
## MT:451_A/AT . 1/1 1/1 .
## MT:499_G/A . . . .
## MT:750_A/G 1/1 1/1 1/1 1/1
## MT:827_A/G . . . .
## MT:1189_T/C . . 0/1 .
## MT:1403_A/G . . . .
## MT:1411_G/T . . . .
## MT:1438_A/G 1/1 1/1 1/1 1/1
## MT:1531_C/T . 0/1 1/1 .
## MT:1537_C/T . . . .
## MT:1608_GTA/G . . . .
## MT:1625_A/G . . . .
## MT:1694_T/C 1/1 . . .
## MT:1750_GAT/G . . 0/1 .
## MT:1842_A/G 0/1 . . .
## MT:1888_G/A 0/1 . . .
## MT:2617_A/G 0/2 1/2 0/1 0/2
## MT:2706_A/G 1/1 0/1 1/1 0/1
## MT:3173_G/A . . . .
## MT:3547_A/G . . . .
## MT:3666_G/A . . . 0/1
## MT:4057_T/C . . . .
## MT:4240_T/C . . . .
## MT:4360_G/A . . . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4820_G/A . . . .
## MT:4917_A/G 0/1 . . .
## MT:4977_T/C . . . .
## MT:5152_T/C . . . .
## MT:6261_G/A 1/1 . . .
## MT:6450_CT/C . . . .
## MT:6473_C/T . . . .
## MT:6646_T/C . . . .
## MT:7028_C/T 1/1 0/1 1/1 1/1
## MT:7223_C/T . . 0/1 .
## MT:7241_A/G . . . .
## MT:8014_A/T . . . 0/1
## MT:8027_G/A . . . .
## MT:8269_G/A . . . .
## MT:8270_CACCCCCTCT/C . . . .
## MT:8271_A/ACCCC . . . 0/1
## MT:8277_T/C . . . 0/1
## MT:8455_C/T 0/1 . . .
## MT:8468_C/T . . . .
## MT:8697_G/A 0/1 . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . 0/1 .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9156_A/G . . 0/1 .
## MT:9950_T/C . . . .
## MT:9966_G/A . . 0/1 .
## MT:9983_A/C . . . .
## MT:10034_T/C . . 0/1 .
## MT:10463_T/C 0/1 . . .
## MT:10685_G/A . 0/1 . .
## MT:10822_C/T 0/1 . . .
## MT:11251_A/G 0/1 . . .
## MT:11425_A/G 0/1 . . .
## MT:11467_A/G . 0/1 . .
## MT:11485_T/C . 0/1 . .
## MT:11719_G/A 1/1 0/1 0/1 0/1
## MT:11812_A/G 0/1 . . .
## MT:12239_C/T . . . .
## MT:12244_G/C . . . .
## MT:12360_C/T 1/1 . . .
## MT:12705_C/T 0/1 0/1 0/1 0/1
## MT:12940_G/A . . 0/1 .
## MT:13368_G/A 0/1 . . .
## MT:13973_A/T 0/1 . . .
## MT:14233_A/G 1/1 . . .
## MT:14577_T/C . . . .
## MT:14755_A/G . . . .
## MT:14757_T/C . . . .
## MT:14766_C/T 1/1 1/1 1/1 .
## MT:14798_T/C . . . .
## MT:14905_G/A 0/1 . . .
## MT:15043_G/A . 0/1 0/1 .
## MT:15218_A/G . . . 0/1
## MT:15301_G/A . 0/1 0/1 .
## MT:15323_G/A . . 0/1 .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . 0/1
## MT:15607_A/G 0/1 . . .
## MT:15706_A/G . . . .
## MT:15884_G/A . . . .
## MT:15928_G/A 1/1 . . .
## MT:15936_A/G . . 0/1 .
## MT:16067_C/T . . . 0/1
## MT:16126_T/C 1/1 . . .
## MT:16129_G/A . . 0/1 .
## MT:16179_C/T . . . 1/1
## MT:16217_T/C . . . .
## MT:16223_C/T . 0/1 1/1 .
## MT:16224_T/C . . . .
## MT:16291_C/T 1/1 . . .
## MT:16292_C/T 1/1 . . .
## MT:16294_C/T 1/1 . . .
## MT:16295_C/T . . . .
## MT:16319_G/A . . . .
## 08436_default 08437_default 08440_default 08441_default
## MT:150_C/T . . . .
## MT:204_T/C 0/1 0/1 0/1 0/1
## MT:250_T/C 0/1 0/1 0/1 0/1
## MT:263_A/G 1/1 1/1 1/1 1/1
## MT:451_A/AT 1/1 1/1 0/1 .
## MT:499_G/A . . . .
## MT:750_A/G 1/1 1/1 1/1 1/1
## MT:827_A/G . . . .
## MT:1189_T/C . . . .
## MT:1403_A/G . 0/1 . .
## MT:1411_G/T . . . 0/1
## MT:1438_A/G 1/1 1/1 1/1 1/1
## MT:1531_C/T 0/1 . 0/1 .
## MT:1537_C/T . 1/1 . .
## MT:1608_GTA/G . . . .
## MT:1625_A/G . . . .
## MT:1694_T/C . . . .
## MT:1750_GAT/G . . . .
## MT:1842_A/G . . . .
## MT:1888_G/A . . . .
## MT:2617_A/G 1/2 1/2 1/2 1/2
## MT:2706_A/G 1/1 1/1 0/1 0/1
## MT:3173_G/A . . . .
## MT:3547_A/G . . . .
## MT:3666_G/A . . . .
## MT:4057_T/C . . . .
## MT:4240_T/C . . . .
## MT:4360_G/A 0/1 . . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4820_G/A . . . .
## MT:4917_A/G . . . .
## MT:4977_T/C . . . .
## MT:5152_T/C . . . .
## MT:6261_G/A . . . .
## MT:6450_CT/C . . . 0/1
## MT:6473_C/T . . . .
## MT:6646_T/C . 0/1 . .
## MT:7028_C/T 0/1 0/1 0/1 1/1
## MT:7223_C/T . . . .
## MT:7241_A/G . . . .
## MT:8014_A/T . . . .
## MT:8027_G/A . . . 0/1
## MT:8269_G/A . . . 0/1
## MT:8270_CACCCCCTCT/C . . . .
## MT:8271_A/ACCCC . . . .
## MT:8277_T/C . . . .
## MT:8455_C/T . . . .
## MT:8468_C/T . . . .
## MT:8697_G/A . . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . 0/1 .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9156_A/G . . . .
## MT:9950_T/C . . . .
## MT:9966_G/A 0/1 . 0/1 .
## MT:9983_A/C . . . 1/1
## MT:10034_T/C 0/1 . . .
## MT:10463_T/C . . . .
## MT:10685_G/A . . . .
## MT:10822_C/T . . . .
## MT:11251_A/G . . . .
## MT:11425_A/G . . . .
## MT:11467_A/G . . . .
## MT:11485_T/C . . . .
## MT:11719_G/A 1/1 0/1 0/1 0/1
## MT:11812_A/G . . . .
## MT:12239_C/T . . . .
## MT:12244_G/C . . . .
## MT:12360_C/T . . . .
## MT:12705_C/T 0/1 0/1 0/1 0/1
## MT:12940_G/A . . . .
## MT:13368_G/A . . . .
## MT:13973_A/T . . . .
## MT:14233_A/G . . . .
## MT:14577_T/C . 0/1 . .
## MT:14755_A/G . . 0/1 .
## MT:14757_T/C . . . .
## MT:14766_C/T 1/1 1/1 1/1 0/1
## MT:14798_T/C . . . .
## MT:14905_G/A . . . .
## MT:15043_G/A 0/1 0/1 0/1 0/1
## MT:15218_A/G . . . .
## MT:15301_G/A 0/1 0/1 0/1 0/1
## MT:15323_G/A . . . .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . .
## MT:15607_A/G . . . .
## MT:15706_A/G . . . .
## MT:15884_G/A . . . .
## MT:15928_G/A . . . .
## MT:15936_A/G . . . .
## MT:16067_C/T . . . .
## MT:16126_T/C . . . .
## MT:16129_G/A 1/1 . . .
## MT:16179_C/T . . . .
## MT:16217_T/C . . . .
## MT:16223_C/T 0/1 . 1/1 1/1
## MT:16224_T/C . 0/1 . .
## MT:16291_C/T . . . .
## MT:16292_C/T . . . .
## MT:16294_C/T . . . .
## MT:16295_C/T . . . .
## MT:16319_G/A . . . 0/1
## 08444_default SLS_default
## MT:150_C/T . .
## MT:204_T/C 0/1 .
## MT:250_T/C 0/1 .
## MT:263_A/G 0/1 1/1
## MT:451_A/AT 0/1 .
## MT:499_G/A . 0/1
## MT:750_A/G 1/1 1/1
## MT:827_A/G . 0/1
## MT:1189_T/C . .
## MT:1403_A/G . .
## MT:1411_G/T . .
## MT:1438_A/G 1/1 1/1
## MT:1531_C/T 1/1 .
## MT:1537_C/T . .
## MT:1608_GTA/G . .
## MT:1625_A/G . .
## MT:1694_T/C . .
## MT:1750_GAT/G . .
## MT:1842_A/G . .
## MT:1888_G/A . .
## MT:2617_A/G 1/2 1/2
## MT:2706_A/G 0/1 1/1
## MT:3173_G/A . .
## MT:3547_A/G . 0/1
## MT:3666_G/A . .
## MT:4057_T/C . .
## MT:4240_T/C . .
## MT:4360_G/A . .
## MT:4769_A/G 1/1 1/1
## MT:4820_G/A . 0/1
## MT:4917_A/G . .
## MT:4977_T/C . 0/1
## MT:5152_T/C . .
## MT:6261_G/A . .
## MT:6450_CT/C . .
## MT:6473_C/T . 0/1
## MT:6646_T/C . .
## MT:7028_C/T 0/1 1/1
## MT:7223_C/T . .
## MT:7241_A/G . 0/1
## MT:8014_A/T . .
## MT:8027_G/A . .
## MT:8269_G/A . .
## MT:8270_CACCCCCTCT/C . 0/1
## MT:8271_A/ACCCC . .
## MT:8277_T/C . .
## MT:8455_C/T . .
## MT:8468_C/T . .
## MT:8697_G/A . .
## MT:8702_C/T . 0/1
## MT:8794_C/T . .
## MT:8860_A/G 1/1 1/1
## MT:9156_A/G . .
## MT:9950_T/C . 0/1
## MT:9966_G/A . .
## MT:9983_A/C . .
## MT:10034_T/C . .
## MT:10463_T/C . .
## MT:10685_G/A . .
## MT:10822_C/T . .
## MT:11251_A/G . .
## MT:11425_A/G . .
## MT:11467_A/G . 0/1
## MT:11485_T/C . 0/1
## MT:11719_G/A 0/1 1/1
## MT:11812_A/G . .
## MT:12239_C/T . .
## MT:12244_G/C 0/1 .
## MT:12360_C/T . .
## MT:12705_C/T 0/1 0/1
## MT:12940_G/A . .
## MT:13368_G/A . .
## MT:13973_A/T . .
## MT:14233_A/G . .
## MT:14577_T/C . .
## MT:14755_A/G . .
## MT:14757_T/C . 0/1
## MT:14766_C/T 0/1 1/1
## MT:14798_T/C 0/1 .
## MT:14905_G/A . .
## MT:15043_G/A 0/1 .
## MT:15218_A/G . .
## MT:15301_G/A 0/1 .
## MT:15323_G/A . .
## MT:15326_A/G 1/1 1/1
## MT:15597_T/G . .
## MT:15607_A/G . .
## MT:15706_A/G . 0/1
## MT:15884_G/A . .
## MT:15928_G/A . .
## MT:15936_A/G . .
## MT:16067_C/T . .
## MT:16126_T/C . .
## MT:16129_G/A 1/1 .
## MT:16179_C/T . .
## MT:16217_T/C . 0/1
## MT:16223_C/T . .
## MT:16224_T/C . .
## MT:16291_C/T . .
## MT:16292_C/T . .
## MT:16294_C/T . .
## MT:16295_C/T . .
## MT:16319_G/A . 0/1mito2 <- mito[names(mito) %in% names(pred2)]
mito_rr <- data.frame(pred2[names(pred2) %in% names(mito2)])
mito_geno <- as.data.frame(geno(mito2)$GT)
mito_df2 <- cbind(mito_rr, mito_geno)
write.table(mito_df2,file="mito_df2.tsv", sep="\t")
mito_df2## seqnames start end width strand paramRangeID REF ALT QUAL
## MT:3547_A/G MT 3547 3547 1 + <NA> A G 44.80
## MT:4057_T/C MT 4057 4057 1 + <NA> T C 7.90
## MT:4240_T/C MT 4240 4240 1 + <NA> T C 10.40
## MT:4769_A/G MT 4769 4769 1 + <NA> A G 33.87
## MT:4917_A/G MT 4917 4917 1 + <NA> A G 40.60
## MT:5152_T/C MT 5152 5152 1 + <NA> T C 6.70
## MT:6261_G/A MT 6261 6261 1 + <NA> G A 46.70
## MT:6450_CT/C MT 6450 6451 2 + <NA> CT C 4.30
## MT:6646_T/C MT 6646 6646 1 + <NA> T C 3.80
## MT:8027_G/A MT 8027 8027 1 + <NA> G A 10.50
## MT:8697_G/A MT 8697 8697 1 + <NA> G A 33.90
## MT:8702_C/T MT 8702 8702 1 + <NA> C T 35.80
## MT:8794_C/T MT 8794 8794 1 + <NA> C T 11.17
## MT:8860_A/G MT 8860 8860 1 + <NA> A G 41.22
## MT:9966_G/A MT 9966 9966 1 + <NA> G A 38.93
## MT:9983_A/C MT 9983 9983 1 + <NA> A C 8.90
## MT:12940_G/A MT 12940 12940 1 + <NA> G A 12.90
## MT:13973_A/T MT 13973 13973 1 + <NA> A T 41.00
## MT:14577_T/C MT 14577 14577 1 - <NA> T C 23.90
## MT:14757_T/C MT 14757 14757 1 + <NA> T C 32.10
## MT:14766_C/T MT 14766 14766 1 + <NA> C T 32.28
## MT:14798_T/C MT 14798 14798 1 + <NA> T C 12.40
## MT:14905_G/A MT 14905 14905 1 + <NA> G A 41.10
## MT:15218_A/G MT 15218 15218 1 + <NA> A G 35.30
## MT:15323_G/A MT 15323 15323 1 + <NA> G A 14.40
## MT:15326_A/G MT 15326 15326 1 + <NA> A G 41.49
## MT:15597_T/G MT 15597 15597 1 + <NA> T G 8.80
## MT:15884_G/A MT 15884 15884 1 + <NA> G A 8.80
## FILTER varAllele CDSLOC.start CDSLOC.end CDSLOC.width PROTEINLOC
## MT:3547_A/G PASS G 241 241 1 81
## MT:4057_T/C PASS C 751 751 1 251
## MT:4240_T/C PASS C 934 934 1 312
## MT:4769_A/G PASS G 300 300 1 100
## MT:4917_A/G PASS G 448 448 1 150
## MT:5152_T/C PASS C 683 683 1 228
## MT:6261_G/A PASS A 358 358 1 120
## MT:6450_CT/C PASS C 547 548 2 183
## MT:6646_T/C PASS C 743 743 1 248
## MT:8027_G/A PASS A 442 442 1 148
## MT:8697_G/A PASS A 171 171 1 57
## MT:8702_C/T PASS T 176 176 1 59
## MT:8794_C/T PASS T 268 268 1 90
## MT:8860_A/G PASS G 334 334 1 112
## MT:9966_G/A PASS A 760 760 1 254
## MT:9983_A/C PASS C 777 777 1 259
## MT:12940_G/A PASS A 604 604 1 202
## MT:13973_A/T PASS T 1637 1637 1 546
## MT:14577_T/C PASS G 97 97 1 33
## MT:14757_T/C PASS C 11 11 1 4
## MT:14766_C/T PASS T 20 20 1 7
## MT:14798_T/C PASS C 52 52 1 18
## MT:14905_G/A PASS A 159 159 1 53
## MT:15218_A/G PASS G 472 472 1 158
## MT:15323_G/A PASS A 577 577 1 193
## MT:15326_A/G PASS G 580 580 1 194
## MT:15597_T/G PASS G 851 851 1 284
## MT:15884_G/A PASS A 1138 1138 1 380
## QUERYID TXID CDSID GENEID CONSEQUENCE REFCODON
## MT:3547_A/G 2448082 251031 277405 ENSG00000198888 nonsynonymous ATC
## MT:4057_T/C 2448084 251031 277405 ENSG00000198888 nonsynonymous TCC
## MT:4240_T/C 2448085 251031 277405 ENSG00000198888 nonsynonymous TCC
## MT:4769_A/G 2448087 251034 277406 ENSG00000198763 nonsynonymous ATA
## MT:4917_A/G 2448089 251034 277406 ENSG00000198763 nonsynonymous AAC
## MT:5152_T/C 2448091 251034 277406 ENSG00000198763 nonsynonymous CTA
## MT:6261_G/A 2448092 251036 277407 ENSG00000198804 nonsynonymous GCC
## MT:6450_CT/C 2448093 251036 277407 ENSG00000198804 frameshift CTC
## MT:6646_T/C 2448095 251036 277407 ENSG00000198804 nonsynonymous CTA
## MT:8027_G/A 2448100 251038 277408 ENSG00000198712 nonsynonymous GCC
## MT:8697_G/A 2448107 251041 277410 ENSG00000198899 nonsynonymous ATG
## MT:8702_C/T 2448108 251041 277410 ENSG00000198899 nonsynonymous ACC
## MT:8794_C/T 2448109 251041 277410 ENSG00000198899 nonsynonymous CAC
## MT:8860_A/G 2448110 251041 277410 ENSG00000198899 nonsynonymous ACA
## MT:9966_G/A 2448113 251042 277411 ENSG00000198938 nonsynonymous GTC
## MT:9983_A/C 2448114 251042 277411 ENSG00000198938 nonsynonymous TGA
## MT:12940_G/A 2448129 251051 277415 ENSG00000198786 nonsynonymous GCC
## MT:13973_A/T 2448131 251051 277415 ENSG00000198786 nonsynonymous CAA
## MT:14577_T/C 2448133 251060 277417 ENSG00000198695 nonsynonymous ATT
## MT:14757_T/C 2448135 251052 277416 ENSG00000198727 nonsynonymous ATA
## MT:14766_C/T 2448136 251052 277416 ENSG00000198727 nonsynonymous ACT
## MT:14798_T/C 2448137 251052 277416 ENSG00000198727 nonsynonymous TTC
## MT:14905_G/A 2448138 251052 277416 ENSG00000198727 nonsynonymous ATG
## MT:15218_A/G 2448140 251052 277416 ENSG00000198727 nonsynonymous ACA
## MT:15323_G/A 2448142 251052 277416 ENSG00000198727 nonsynonymous GCA
## MT:15326_A/G 2448143 251052 277416 ENSG00000198727 nonsynonymous ACA
## MT:15597_T/G 2448144 251052 277416 ENSG00000198727 nonsynonymous GTC
## MT:15884_G/A 2448147 251052 277416 ENSG00000198727 nonsynonymous GCC
## VARCODON REFAA VARAA default 08407_default 08409_default
## MT:3547_A/G GTC I V . . .
## MT:4057_T/C CCC S P . . 0/1
## MT:4240_T/C CCC S P . . .
## MT:4769_A/G ATG I M 1/1 1/1 1/1
## MT:4917_A/G GAC N D . . .
## MT:5152_T/C CCA L P . . .
## MT:6261_G/A ACC A T . . .
## MT:6450_CT/C CC . . .
## MT:6646_T/C CCA L P . . .
## MT:8027_G/A ACC A T . . .
## MT:8697_G/A ATA M I . . .
## MT:8702_C/T ATC T I . . .
## MT:8794_C/T TAC H Y 0/1 . .
## MT:8860_A/G GCA T A 1/1 1/1 1/1
## MT:9966_G/A ATC V I 0/1 . .
## MT:9983_A/C TGC * C . . .
## MT:12940_G/A ACC A T . . .
## MT:13973_A/T CTA Q L . . .
## MT:14577_T/C GTT I V . . .
## MT:14757_T/C ACA I T . . .
## MT:14766_C/T ATT T I 0/1 0/1 1/1
## MT:14798_T/C CTC F L . . .
## MT:14905_G/A ATA M I . . .
## MT:15218_A/G GCA T A . . .
## MT:15323_G/A ACA A T . 0/1 .
## MT:15326_A/G GCA T A 1/1 1/1 1/1
## MT:15597_T/G GGC V G . . .
## MT:15884_G/A ACC A T . . .
## 08415_default 08416_default 08417_default 08418_default
## MT:3547_A/G . . . .
## MT:4057_T/C . . . .
## MT:4240_T/C . . . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4917_A/G . . . .
## MT:5152_T/C . . . .
## MT:6261_G/A . . . .
## MT:6450_CT/C . . . .
## MT:6646_T/C . . . .
## MT:8027_G/A . . . .
## MT:8697_G/A . . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . . .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9966_G/A 0/1 0/1 0/1 0/1
## MT:9983_A/C . . . .
## MT:12940_G/A . . . .
## MT:13973_A/T . . . .
## MT:14577_T/C . . . .
## MT:14757_T/C . . . .
## MT:14766_C/T 1/1 0/1 0/1 1/1
## MT:14798_T/C . . . .
## MT:14905_G/A . . . .
## MT:15218_A/G . . . .
## MT:15323_G/A . . . .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . .
## MT:15884_G/A . . . .
## 08420_default 08421_default 08422_default 08423_default
## MT:3547_A/G . . . .
## MT:4057_T/C . . . .
## MT:4240_T/C . 0/1 . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4917_A/G . . . .
## MT:5152_T/C 0/1 . . .
## MT:6261_G/A . . . .
## MT:6450_CT/C . . . .
## MT:6646_T/C . . . .
## MT:8027_G/A . . . .
## MT:8697_G/A . . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . . .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9966_G/A 0/1 0/1 0/1 0/1
## MT:9983_A/C . . . .
## MT:12940_G/A . . . .
## MT:13973_A/T . . . .
## MT:14577_T/C . . . .
## MT:14757_T/C . . . .
## MT:14766_C/T 0/1 0/1 1/1 1/1
## MT:14798_T/C . . . .
## MT:14905_G/A . . . .
## MT:15218_A/G . . . .
## MT:15323_G/A . . . .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . .
## MT:15884_G/A . . . 0/1
## 08429_default 08431_default 08433_default 08435_default
## MT:3547_A/G . . . .
## MT:4057_T/C . . . .
## MT:4240_T/C . . . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4917_A/G 0/1 . . .
## MT:5152_T/C . . . .
## MT:6261_G/A 1/1 . . .
## MT:6450_CT/C . . . .
## MT:6646_T/C . . . .
## MT:8027_G/A . . . .
## MT:8697_G/A 0/1 . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . 0/1 .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9966_G/A . . 0/1 .
## MT:9983_A/C . . . .
## MT:12940_G/A . . 0/1 .
## MT:13973_A/T 0/1 . . .
## MT:14577_T/C . . . .
## MT:14757_T/C . . . .
## MT:14766_C/T 1/1 1/1 1/1 .
## MT:14798_T/C . . . .
## MT:14905_G/A 0/1 . . .
## MT:15218_A/G . . . 0/1
## MT:15323_G/A . . 0/1 .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . 0/1
## MT:15884_G/A . . . .
## 08436_default 08437_default 08440_default 08441_default
## MT:3547_A/G . . . .
## MT:4057_T/C . . . .
## MT:4240_T/C . . . .
## MT:4769_A/G 1/1 1/1 1/1 1/1
## MT:4917_A/G . . . .
## MT:5152_T/C . . . .
## MT:6261_G/A . . . .
## MT:6450_CT/C . . . 0/1
## MT:6646_T/C . 0/1 . .
## MT:8027_G/A . . . 0/1
## MT:8697_G/A . . . .
## MT:8702_C/T . . . .
## MT:8794_C/T . . 0/1 .
## MT:8860_A/G 1/1 1/1 1/1 1/1
## MT:9966_G/A 0/1 . 0/1 .
## MT:9983_A/C . . . 1/1
## MT:12940_G/A . . . .
## MT:13973_A/T . . . .
## MT:14577_T/C . 0/1 . .
## MT:14757_T/C . . . .
## MT:14766_C/T 1/1 1/1 1/1 0/1
## MT:14798_T/C . . . .
## MT:14905_G/A . . . .
## MT:15218_A/G . . . .
## MT:15323_G/A . . . .
## MT:15326_A/G 1/1 1/1 1/1 1/1
## MT:15597_T/G . . . .
## MT:15884_G/A . . . .
## 08444_default SLS_default
## MT:3547_A/G . 0/1
## MT:4057_T/C . .
## MT:4240_T/C . .
## MT:4769_A/G 1/1 1/1
## MT:4917_A/G . .
## MT:5152_T/C . .
## MT:6261_G/A . .
## MT:6450_CT/C . .
## MT:6646_T/C . .
## MT:8027_G/A . .
## MT:8697_G/A . .
## MT:8702_C/T . 0/1
## MT:8794_C/T . .
## MT:8860_A/G 1/1 1/1
## MT:9966_G/A . .
## MT:9983_A/C . .
## MT:12940_G/A . .
## MT:13973_A/T . .
## MT:14577_T/C . .
## MT:14757_T/C . 0/1
## MT:14766_C/T 0/1 1/1
## MT:14798_T/C 0/1 .
## MT:14905_G/A . .
## MT:15218_A/G . .
## MT:15323_G/A . .
## MT:15326_A/G 1/1 1/1
## MT:15597_T/G . .
## MT:15884_G/A . .Look for causative mutations
Suspecting homozygous recessive mutation as causing LHON in this pedigree as it involves a consanguineous marriage.
Screen variants that are:
Homozygous in 08407, 08422, 08433, 08440, and 08441; and
Heterozygous or homozygous reference in all others; 8409, 08415, 08416, 08417, 08418, 08420, 08421, 08423, 08429, 08431, 08435, 08436, 08437 and 08444.
gt <- geno(vcf)$GT
aff <- ss[which(ss$Diagnosis == "affected"),1]
gt_aff <- gt[,which(colnames(gt) %in% aff)]
unaff <- ss[which(ss$Diagnosis == "unaffected"),1]
gt_unaff <- gt[,which(colnames(gt) %in% unaff)]
cnt_aff <- apply(gt_aff,1,function(x) { length(which(x=="1/1")) } )
table(cnt_aff)## cnt_aff
## 0 1 2 3 4 5
## 1747632 563682 117041 47597 24169 22434cnt_unaff <- apply(gt_unaff,1,function(x) { length(which(x!="1/1")) } )
table(cnt_unaff)## cnt_unaff
## 0 1 2 3 4 5 6 7 8 9 10
## 12927 6649 6499 7393 9061 11443 15002 19989 27216 39831 61054
## 11 12 13 14
## 105609 224708 975359 999815vars <- which(cnt_aff == max(cnt_aff) & cnt_unaff == max(cnt_unaff))
vars## 10:123560788_A/G 12:29725397_C/G 14:64796285_G/C 19:3319213_G/A
## 322899 485699 687744 1075911
## 7:67833867_G/A 8:140329893_T/C
## 2146561 2332278which( names(pred) %in% names(vars) )## integer(0)None of these variants are located in an exon, and they apper to be too frequent in the population to be plausibly linked to a disease.
Now let’s look at the variants where one of the unaffected individuals might actually be homozygous.
vars <- which(cnt_aff == max(cnt_aff) & cnt_unaff == (max(cnt_unaff)-1) )
vars## 1:15293508_G/A 1:154521606_G/C 10:114762268_T/C
## 21545 124024 313462
## 12:97275481_A/G 16:84510657_C/G 17:49126028_GATGACAA/G
## 534905 892194 963554
## 18:2276070_T/C 2:186343856_T/C 5:179286382_A/G
## 1008503 1307394 1932718
## 6:33389832_A/G 8:140548881_C/T
## 1979280 2332561which( names(pred) %in% names(vars) )## integer(0)Now let’s look at the variants where two of the unaffected individuals might actually be homozygous for the variant.
vars <- which(cnt_aff == max(cnt_aff) & cnt_unaff >= (max(cnt_unaff)-2) )
vars## 1:15293508_G/A 1:27836821_G/C 1:154521606_G/C
## 21545 40470 124024
## 1:157132133_C/G 1:181275732_T/C 10:114762268_T/C
## 127291 147647 313462
## 10:119033172_A/G 10:123560788_A/G 11:122666713_A/G
## 317183 322899 444522
## 12:3605001_A/G 12:29725397_C/G 12:56510703_G/A
## 461539 485699 508943
## 12:97275481_A/G 14:64796285_G/C 14:77726470_T/G
## 534905 687744 701082
## 16:84510657_C/G 16:86526211_C/T 17:45834350_G/T
## 892194 896322 958911
## 17:47808390_C/T 17:49126028_GATGACAA/G 18:2276070_T/C
## 961722 963554 1008503
## 18:77088204_A/C 19:3319213_G/A 2:186343856_T/C
## 1063148 1075911 1307394
## 21:16026471_T/C 22:11054967_A/C 3:193362960_C/A
## 1430272 1461402 1656259
## 4:827452_T/C 4:43030595_G/A 5:177581082_A/T
## 1664588 1705675 1929457
## 5:179286382_A/G 6:33389832_A/G 6:89258136_C/T
## 1932718 1979280 2020941
## 7:7279368_A/C 7:48587049_C/G 7:67833867_G/A
## 2096061 2129624 2146561
## 7:139034448_AG/A 8:140329893_T/C 8:140548881_C/T
## 2201379 2332278 2332561
## 8:140551112_A/G 9:124066361_T/C
## 2332570 2424579which( names(pred) %in% names(vars) )## [1] 22297pred[which( names(pred) %in% names(vars) )]## GRanges object with 1 range and 17 metadata columns:
## seqnames ranges strand | paramRangeID REF
## <Rle> <IRanges> <Rle> | <factor> <DNAStringSet>
## 17:47808390_C/T 17 47808390 - | NA C
## ALT QUAL FILTER varAllele
## <DNAStringSetList> <numeric> <character> <DNAStringSet>
## 17:47808390_C/T T 57.19 PASS A
## CDSLOC PROTEINLOC QUERYID TXID CDSID
## <IRanges> <IntegerList> <integer> <character> <IntegerList>
## 17:47808390_C/T 2430 810 961722 205442 227172
## GENEID CONSEQUENCE REFCODON VARCODON
## <character> <factor> <DNAStringSet> <DNAStringSet>
## 17:47808390_C/T ENSG00000006025 synonymous ACG ACA
## REFAA VARAA
## <AAStringSet> <AAStringSet>
## 17:47808390_C/T T T
## -------
## seqinfo: 40 sequences from GRCh38 genomeNow let’s look at the variants where three of the unaffected individuals might actually be homozygous for the variant.
vars <- which(cnt_aff == max(cnt_aff) & cnt_unaff >= (max(cnt_unaff)-3) )
vars## 1:4762628_A/G 1:15293508_G/A 1:27836821_G/C
## 7521 21545 40470
## 1:54432888_C/T 1:75979828_G/A 1:154521606_G/C
## 68312 83487 124024
## 1:157132133_C/G 1:181275732_T/C 1:200941198_T/G
## 127291 147647 159414
## 1:204577819_T/C 1:213598716_A/G 1:234906380_A/G
## 164562 173256 192001
## 10:1556523_G/A 10:1557135_GC/G 10:3413349_A/C
## 210277 210278 213025
## 10:48481079_G/A 10:59696932_TG/T 10:97199769_T/C
## 256536 264362 298109
## 10:114762268_T/C 10:119033172_A/G 10:123560788_A/G
## 313462 317183 322899
## 11:13963418_A/G 11:17847126_T/C 11:66050231_T/C
## 357156 360234 397419
## 11:77282478_A/AC 11:122666713_A/G 11:130582764_T/C
## 410523 444522 452134
## 12:3605001_A/G 12:29725397_C/G 12:56510703_G/A
## 461539 485699 508943
## 12:57714269_C/T 12:94277573_T/C 12:94277635_C/T
## 510293 531503 531504
## 12:97275481_A/G 12:120975001_G/C 12:124426924_A/G
## 534905 557154 562641
## 13:20124813_T/C 13:20946064_C/T 13:61418900_T/A
## 578995 580266 613769
## 13:67005977_A/G 13:106864432_A/G 14:52157869_G/C
## 616315 642097 677477
## 14:52157921_A/G 14:64784038_A/G 14:64796285_G/C
## 677479 687723 687744
## 14:77726470_T/G 15:20301361_T/C 15:98634366_C/G
## 701082 732792 806359
## 16:10087727_T/C 16:26724912_G/A 16:26724913_T/A
## 828574 847597 847598
## 16:56683597_T/C 16:84510657_C/G 16:86526211_C/T
## 863181 892194 896322
## 17:45834350_G/T 17:47808390_C/T 17:49126028_GATGACAA/G
## 958911 961722 963554
## 17:66304015_C/T 17:67753706_A/G 17:78537187_A/AAAAG
## 979444 981168 996300
## 18:2276070_T/C 18:77088204_A/C 19:736447_A/G
## 1008503 1063148 1069462
## 19:3319213_G/A 2:24371079_G/A 2:42851315_A/G
## 1075911 1189555 1207157
## 2:186343856_T/C 2:238165293_T/C 2:240711193_A/G
## 1307394 1350979 1354717
## 2:241437825_T/C 20:1281775_G/A 21:16026471_T/C
## 1355818 1358807 1430272
## 21:31182220_C/T 21:42987195_A/G 22:11054967_A/C
## 1439929 1454285 1461402
## 22:12693186_T/C 22:23502179_G/A 22:38284355_T/C
## 1462806 1474463 1493728
## 22:45545927_T/C 3:38477933_A/G 3:38479934_C/T
## 1505467 1546499 1546503
## 3:38580976_T/C 3:38587170_C/A 3:107331739_G/A
## 1546614 1546627 1594309
## 3:109892088_G/C 3:193362960_C/A 4:827452_T/C
## 1596233 1656259 1664588
## 4:6383806_T/C 4:8226707_A/G 4:8287526_G/C
## 1674016 1677917 1678098
## 4:8287529_A/G 4:43030595_G/A 4:44689189_TA/T
## 1678099 1705675 1706669
## 4:52995418_A/C 4:157691413_A/G 5:154007031_A/G
## 1711025 1776989 1909602
## 5:177581082_A/T 5:179286382_A/G 6:32325793_G/A
## 1929457 1932718 1974700
## 6:32530535_C/T 6:33389832_A/G 6:41230407_G/A
## 1975640 1979280 1989319
## 6:89258136_C/T 6:158148854_T/C 7:7279368_A/C
## 2020941 2066371 2096061
## 7:15447781_A/G 7:48587049_C/G 7:50477268_G/A
## 2101562 2129624 2130815
## 7:65073773_T/C 7:67833867_G/A 7:75482661_A/G
## 2142525 2146561 2155459
## 7:139034448_AG/A 8:80053037_A/G 8:132971710_A/G
## 2201379 2292156 2325343
## 8:132972774_G/A 8:132972814_A/G 8:132983131_A/G
## 2325348 2325349 2325366
## 8:132983230_A/G 8:140329893_T/C 8:140544575_TCAGGCC/T
## 2325368 2332278 2332555
## 8:140548881_C/T 8:140551112_A/G 9:6504189_A/C
## 2332561 2332570 2346990
## 9:36265162_G/A 9:114102993_T/C 9:124066361_T/C
## 2369702 2416658 2424579
## X:155451167_C/T KI270728.1:1561554_A/G
## 2514986 2518147which( names(pred) %in% names(vars) )## [1] 22297 36679 36685pred[which( names(pred) %in% names(vars) )]## GRanges object with 3 ranges and 17 metadata columns:
## seqnames ranges strand | paramRangeID REF
## <Rle> <IRanges> <Rle> | <factor> <DNAStringSet>
## 17:47808390_C/T 17 47808390 - | NA C
## 3:38477933_A/G 3 38477933 + | NA A
## 3:38580976_T/C 3 38580976 - | NA T
## ALT QUAL FILTER varAllele
## <DNAStringSetList> <numeric> <character> <DNAStringSet>
## 17:47808390_C/T T 57.19 PASS A
## 3:38477933_A/G G 48.94 PASS G
## 3:38580976_T/C C 52.11 PASS G
## CDSLOC PROTEINLOC QUERYID TXID CDSID
## <IRanges> <IntegerList> <integer> <character> <IntegerList>
## 17:47808390_C/T 2430 810 961722 205442 227172
## 3:38477933_A/G 333 111 1546499 42900 49239
## 3:38580976_T/C 3183 1061 1546614 50615 56827
## GENEID CONSEQUENCE REFCODON VARCODON
## <character> <factor> <DNAStringSet> <DNAStringSet>
## 17:47808390_C/T ENSG00000006025 synonymous ACG ACA
## 3:38477933_A/G ENSG00000114739 synonymous GAA GAG
## 3:38580976_T/C ENSG00000183873 synonymous GAA GAG
## REFAA VARAA
## <AAStringSet> <AAStringSet>
## 17:47808390_C/T T T
## 3:38477933_A/G E E
## 3:38580976_T/C E E
## -------
## seqinfo: 40 sequences from GRCh38 genomeNow let’s look at the variants where four of the unaffected individuals might actually be homozygous for the variant.
vars <- which(cnt_aff == max(cnt_aff) & cnt_unaff >= (max(cnt_unaff)-4) )
vars## 1:2268902_G/T 1:4762628_A/G
## 3152 7521
## 1:6036648_T/C 1:15293508_G/A
## 9018 21545
## 1:21515417_A/C 1:27414637_T/C
## 31868 40148
## 1:27836821_G/C 1:54432888_C/T
## 40470 68312
## 1:67686755_C/T 1:75979828_G/A
## 79220 83487
## 1:87751619_A/G 1:106415898_C/T
## 90976 102831
## 1:109091313_T/G 1:154521606_G/C
## 104694 124024
## 1:157132133_C/G 1:158056614_G/A
## 127291 128151
## 1:159943598_G/A 1:159953169_C/T
## 129841 129852
## 1:181275732_T/C 1:200941198_T/G
## 147647 159414
## 1:204577819_T/C 1:213598716_A/G
## 164562 173256
## 1:234906380_A/G 1:241651974_C/T
## 192001 199487
## 10:277343_A/G 10:1185195_C/T
## 208291 209649
## 10:1556523_G/A 10:1557135_GC/G
## 210277 210278
## 10:2013955_C/G 10:3413349_A/C
## 210939 213025
## 10:5638054_G/A 10:38739981_G/C
## 215622 249247
## 10:48481078_C/A 10:48481079_G/A
## 256535 256536
## 10:59696932_TG/T 10:71271628_C/T
## 264362 275545
## 10:71286342_A/G 10:97199769_T/C
## 275591 298109
## 10:103879663_G/A 10:114762268_T/C
## 305760 313462
## 10:119033172_A/G 10:123560788_A/G
## 317183 322899
## 11:13963418_A/G 11:17847126_T/C
## 357156 360234
## 11:66050231_T/C 11:74646319_A/C
## 397419 407809
## 11:77282478_A/AC 11:122666713_A/G
## 410523 444522
## 11:130582764_T/C 12:721129_C/T
## 452134 457446
## 12:3605001_A/G 12:29725397_C/G
## 461539 485699
## 12:39186997_A/G 12:48717052_A/G
## 492569 499422
## 12:54373659_A/G 12:56510703_G/A
## 506887 508943
## 12:57714269_C/T 12:94277573_T/C
## 510293 531503
## 12:94277635_C/T 12:94759659_G/A
## 531504 531968
## 12:97275481_A/G 12:97438100_G/A
## 534905 535005
## 12:120975001_G/C 12:124426924_A/G
## 557154 562641
## 12:126633137_A/G 13:20124813_T/C
## 565416 578995
## 13:20946064_C/T 13:21478289_T/C
## 580266 581230
## 13:42181702_T/C 13:61418900_T/A
## 600941 613769
## 13:67005977_A/G 13:73220797_A/G
## 616315 619740
## 13:106864432_A/G 14:20837334_C/T
## 642097 654008
## 14:24350702_T/C 14:52157869_G/C
## 658816 677477
## 14:52157921_A/G 14:64779905_T/C
## 677479 687704
## 14:64784038_A/G 14:64786514_T/C
## 687723 687728
## 14:64795707_C/A 14:64796285_G/C
## 687743 687744
## 14:77726470_T/G 14:90522998_A/G
## 701082 709678
## 15:20301361_T/C 15:28282892_C/T
## 732792 740065
## 15:29107922_C/T 15:40908833_G/A
## 740709 751002
## 15:50326074_A/AT 15:98634366_C/G
## 758599 806359
## 16:1364667_TG/T 16:3676364_CGGGCGGGGGGCGGGG/C
## 814193 818174
## 16:10087727_T/C 16:26724912_G/A
## 828574 847597
## 16:26724913_T/A 16:53602021_A/T
## 847598 859893
## 16:54582995_C/T 16:54931629_C/G
## 860876 861140
## 16:56683597_T/C 16:81744616_T/C
## 863181 887699
## 16:84510657_C/G 16:86437981_G/C
## 892194 896152
## 16:86526211_C/T 16:88667077_G/C
## 896322 900591
## 17:4423213_T/G 17:45834350_G/T
## 912650 958911
## 17:47808390_C/T 17:49126028_GATGACAA/G
## 961722 963554
## 17:66304015_C/T 17:67753706_A/G
## 979444 981168
## 17:78537187_A/AAAAG 17:81228665_A/G
## 996300 1001883
## 18:2276070_T/C 18:14154855_A/AC
## 1008503 1021547
## 18:77088204_A/C 19:736447_A/G
## 1063148 1069462
## 19:2467425_T/C 19:3319213_G/A
## 1073629 1075911
## 19:6524080_G/C 19:8608714_T/C
## 1082483 1087742
## 19:13703873_T/C 19:35554733_T/TGTAG
## 1096344 1125355
## 19:35555986_C/CTGACAT 19:38921076_C/CACACAGAT
## 1125357 1130065
## 19:50299352_C/T 19:50592782_TCCTC/T
## 1148996 1149543
## 19:53621569_A/G 2:20646568_A/C
## 1156240 1186918
## 2:24371079_G/A 2:28365753_A/G
## 1189555 1193664
## 2:39448655_A/G 2:42851315_A/G
## 1204362 1207157
## 2:74886530_C/T 2:85322404_T/C
## 1231933 1237501
## 2:113429002_T/C 2:128440796_A/G
## 1257448 1269199
## 2:152178037_C/G 2:152578774_G/A
## 1284761 1285181
## 2:186343856_T/C 2:224655198_T/C
## 1307394 1336288
## 2:238165293_T/C 2:240711193_A/G
## 1350979 1354717
## 2:241437825_T/C 20:1281775_G/A
## 1355818 1358807
## 20:8495670_T/TA 20:11473081_A/T
## 1366907 1368842
## 20:18548463_G/C 20:50004150_A/G
## 1374405 1405326
## 21:16026471_T/C 21:31182220_C/T
## 1430272 1439929
## 21:37169654_G/GC 21:42987195_A/G
## 1446531 1454285
## 21:46648816_G/A 22:11054967_A/C
## 1460484 1461402
## 22:12693186_T/C 22:18492421_A/C
## 1462806 1466558
## 22:23502179_G/A 22:36408608_A/G
## 1474463 1490428
## 22:38284355_T/C 22:43580795_G/A
## 1493728 1501463
## 22:45545927_T/C 22:48646388_T/G
## 1505467 1510374
## 3:36824976_T/C 3:38477933_A/G
## 1545205 1546499
## 3:38479934_C/T 3:38580976_T/C
## 1546503 1546614
## 3:38587170_C/A 3:40261713_A/G
## 1546627 1548086
## 3:44338357_C/G 3:45577262_G/A
## 1551153 1552489
## 3:57070694_A/C 3:65769411_A/C
## 1564007 1571234
## 3:75631695_A/G 3:88280036_C/T
## 1579106 1585185
## 3:107331739_G/A 3:109892088_G/C
## 1594309 1596233
## 3:154312560_C/T 3:183096064_A/G
## 1629916 1646701
## 3:193362960_C/A 4:827452_T/C
## 1656259 1664588
## 4:6383806_T/C 4:8215937_C/CCG
## 1674016 1677883
## 4:8226707_A/G 4:8287526_G/C
## 1677917 1678098
## 4:8287529_A/G 4:13933947_C/T
## 1678099 1684049
## 4:15478601_A/C 4:15964997_G/A
## 1685162 1685645
## 4:28407245_A/G 4:29614269_A/C
## 1694545 1695219
## 4:43030595_G/A 4:44689189_TA/T
## 1705675 1706669
## 4:52995418_A/C 4:62809134_T/C
## 1711025 1718405
## 4:76547632_A/G 4:78587821_C/T
## 1728555 1730360
## 4:78611975_T/G 4:150008974_C/T
## 1730389 1771548
## 4:157691413_A/G 4:158643767_A/G
## 1776989 1777575
## 5:10573402_G/A 5:10624775_T/C
## 1816798 1816864
## 5:14751290_C/T 5:21076245_T/C
## 1819872 1824369
## 5:134058537_A/G 5:136978443_C/CA
## 1892795 1895356
## 5:154007031_A/G 5:169708658_A/G
## 1909602 1920871
## 5:173067873_A/G 5:177581082_A/T
## 1924449 1929457
## 5:179286382_A/G 5:179821774_A/C
## 1932718 1933775
## 5:180607374_G/C 6:29538483_T/C
## 1935153 1965238
## 6:32325793_G/A 6:32442360_T/C
## 1974700 1975241
## 6:32442799_T/C 6:32443164_T/C
## 1975245 1975247
## 6:32443258_A/C 6:32443869_T/G
## 1975249 1975255
## 6:32460012_T/C 6:32530535_C/T
## 1975378 1975640
## 6:33389832_A/G 6:41230407_G/A
## 1979280 1989319
## 6:46816446_A/G 6:51436757_C/G
## 1995391 1998251
## 6:72859742_G/C 6:89258136_C/T
## 2010367 2020941
## 6:106594988_T/G 6:152143704_A/G
## 2030131 2061133
## 6:152145751_A/G 6:158148854_T/C
## 2061139 2066371
## 6:169969619_C/T 7:7279368_A/C
## 2080394 2096061
## 7:9624770_G/C 7:15447781_A/G
## 2097908 2101562
## 7:20742696_T/C 7:20742851_T/C
## 2104718 2104719
## 7:27644410_G/C 7:27857297_C/T
## 2111069 2111254
## 7:48587049_C/G 7:50477268_G/A
## 2129624 2130815
## 7:65073773_T/C 7:67833867_G/A
## 2142525 2146561
## 7:75482661_A/G 7:100976343_T/C
## 2155459 2173421
## 7:138146614_C/T 7:139034448_AG/A
## 2200184 2201379
## 8:13063847_T/G 8:15169159_C/T
## 2243431 2245471
## 8:27453814_T/C 8:74179581_T/G
## 2258699 2289512
## 8:80053037_A/G 8:82048808_G/A
## 2292156 2293614
## 8:82048809_C/T 8:97876572_G/C
## 2293615 2302605
## 8:100269010_C/A 8:129835929_T/C
## 2304075 2322884
## 8:132971710_A/G 8:132972774_G/A
## 2325343 2325348
## 8:132972814_A/G 8:132983131_A/G
## 2325349 2325366
## 8:132983230_A/G 8:140329893_T/C
## 2325368 2332278
## 8:140544575_TCAGGCC/T 8:140547398_T/C
## 2332555 2332558
## 8:140548881_C/T 8:140549026_A/G
## 2332561 2332562
## 8:140549259_G/A 8:140551112_A/G
## 2332564 2332570
## 8:140551294_G/C 8:140555793_A/C
## 2332571 2332580
## 8:140556212_C/T 8:140556388_G/A
## 2332581 2332582
## 8:140558205_A/G 8:140558523_G/A
## 2332586 2332587
## 8:140558600_A/G 8:140558626_G/A
## 2332588 2332589
## 9:6504189_A/C 9:34326122_T/C
## 2346990 2367668
## 9:36265162_G/A 9:98192481_C/CCGGGGGGG
## 2369702 2403510
## 9:114102993_T/C 9:114205672_T/C
## 2416658 2416817
## 9:123440272_A/C 9:124066361_T/C
## 2424133 2424579
## 9:136510909_A/G 9:136511049_A/G
## 2445108 2445109
## 9:136513000_C/T X:71594286_C/T
## 2445114 2482978
## X:152650860_G/A X:155451167_C/T
## 2513260 2514986
## KI270728.1:1561554_A/G
## 2518147which( names(pred) %in% names(vars) )## [1] 5482 15628 15632 22297 30210 36679 36685 41073 44443 44444 46168 50548
## [13] 50549 50550data.frame(pred[which( names(pred) %in% names(vars) )])## seqnames start end width strand paramRangeID REF ALT QUAL FILTER
## 1 10 277343 277343 1 - <NA> A G 51.82 PASS
## 2 14 64779905 64779905 1 - <NA> T C 49.85 PASS
## 3 14 64786514 64786514 1 - <NA> T C 54.12 PASS
## 4 17 47808390 47808390 1 - <NA> C T 57.19 PASS
## 5 2 74886530 74886530 1 + <NA> C T 50.38 PASS
## 6 3 38477933 38477933 1 + <NA> A G 48.94 PASS
## 7 3 38580976 38580976 1 - <NA> T C 52.11 PASS
## 8 5 10624775 10624775 1 + <NA> T C 52.12 PASS
## 9 6 32443258 32443258 1 + <NA> A C 50.43 PASS
## 10 6 32443869 32443869 1 + <NA> T G 47.92 PASS
## 11 6 152143704 152143704 1 - <NA> A G 50.28 PASS
## 12 8 140549259 140549259 1 - <NA> G A 48.82 PASS
## 13 8 140556212 140556212 1 - <NA> C T 50.72 PASS
## 14 8 140558523 140558523 1 - <NA> G A 48.95 PASS
## varAllele CDSLOC.start CDSLOC.end CDSLOC.width PROTEINLOC QUERYID TXID
## 1 C 4596 4596 1 1532 208291 126639
## 2 G 4293 4293 1 1431 687704 171301
## 3 G 3451 3451 1 1151 687728 171301
## 4 A 2430 2430 1 810 961722 205442
## 5 T 2076 2076 1 692 1231933 25352
## 6 G 333 333 1 111 1546499 42900
## 7 G 3183 3183 1 1061 1546614 50615
## 8 C 547 547 1 183 1816864 67647
## 9 C 402 402 1 134 1975249 81122
## 10 G 649 649 1 217 1975255 81121
## 11 C 1572 1572 1 524 2061133 90352
## 12 T 1443 1443 1 481 2332564 112703
## 13 A 1101 1101 1 367 2332581 112703
## 14 T 840 840 1 280 2332587 112703
## CDSID GENEID CONSEQUENCE REFCODON VARCODON REFAA VARAA
## 1 138097 ENSG00000151240 synonymous TAT TAC Y Y
## 2 187655 ENSG00000070182 synonymous CGA CGG R R
## 3 187661 ENSG00000070182 nonsynonymous AAT GAT N D
## 4 227172 ENSG00000006025 synonymous ACG ACA T T
## 5 30016 ENSG00000159399 synonymous AAC AAT N N
## 6 49239 ENSG00000114739 synonymous GAA GAG E E
## 7 56827 ENSG00000183873 synonymous GAA GAG E E
## 8 74880 ENSG00000164236 nonsynonymous TCT CCT S P
## 9 88152 ENSG00000204287 synonymous ATA ATC I I
## 10 88154 ENSG00000204287 nonsynonymous TTG GTG L V
## 11 98924 ENSG00000131018 synonymous CGT CGC R R
## 12 121217 ENSG00000123908 synonymous GCC GCT A A
## 13 121220 ENSG00000123908 synonymous GCG GCA A A
## 14 121222 ENSG00000123908 synonymous CGC CGT R Rdata.frame(pred2[which( names(pred2) %in% names(vars) )])## seqnames start end width strand paramRangeID REF ALT QUAL FILTER
## 1 14 64786514 64786514 1 - <NA> T C 54.12 PASS
## 2 5 10624775 10624775 1 + <NA> T C 52.12 PASS
## 3 6 32443869 32443869 1 + <NA> T G 47.92 PASS
## varAllele CDSLOC.start CDSLOC.end CDSLOC.width PROTEINLOC QUERYID TXID
## 1 G 3451 3451 1 1151 687728 171301
## 2 C 547 547 1 183 1816864 67647
## 3 G 649 649 1 217 1975255 81121
## CDSID GENEID CONSEQUENCE REFCODON VARCODON REFAA VARAA
## 1 187661 ENSG00000070182 nonsynonymous AAT GAT N D
## 2 74880 ENSG00000164236 nonsynonymous TCT CCT S P
## 3 88154 ENSG00000204287 nonsynonymous TTG GTG L VNow let’s look at the variants where five of the unaffected individuals might actually be homozygous for the variant.
vars <- which(cnt_aff == max(cnt_aff) & cnt_unaff >= (max(cnt_unaff)-5) )
vars## 1:1925261_C/T 1:1954946_T/C
## 2450 2553
## 1:2035220_A/G 1:2268902_G/T
## 2778 3152
## 1:4762628_A/G 1:6036648_T/C
## 7521 9018
## 1:14023121_T/C 1:15293508_G/A
## 19963 21545
## 1:21424477_T/A 1:21428642_T/G
## 31652 31683
## 1:21428854_C/T 1:21473726_C/T
## 31687 31772
## 1:21515417_A/C 1:21868184_A/G
## 31868 32538
## 1:27414637_T/C 1:27836821_G/C
## 40148 40470
## 1:27959121_A/T 1:32651022_T/G
## 40715 46395
## 1:33312625_G/A 1:33329930_G/C
## 47142 47160
## 1:36286832_C/T 1:36301374_G/C
## 49990 50013
## 1:36301799_C/T 1:43222649_C/T
## 50014 58035
## 1:43300755_A/G 1:54432888_C/T
## 58145 68312
## 1:67686705_T/C 1:67686755_C/T
## 79219 79220
## 1:75979828_G/A 1:87751619_A/G
## 83487 90976
## 1:102749492_A/G 1:106415898_C/T
## 100978 102831
## 1:109091313_T/G 1:143600192_T/C
## 104694 115599
## 1:154355321_T/C 1:154521606_G/C
## 123765 124024
## 1:157132133_C/G 1:158056614_G/A
## 127291 128151
## 1:159943598_G/A 1:159953169_C/T
## 129841 129852
## 1:160166560_G/A 1:178684145_C/T
## 130129 144657
## 1:181275732_T/C 1:200941198_T/G
## 147647 159414
## 1:203665568_A/G 1:204577819_T/C
## 163196 164562
## 1:213598716_A/G 1:221137403_G/C
## 173256 178144
## 1:227732360_T/G 1:227747579_C/T
## 184777 184796
## 1:227747654_T/C 1:227758800_G/GCC
## 184797 184813
## 1:227780332_T/C 1:234906380_A/G
## 184842 192001
## 1:236620311_A/G 1:240230179_T/C
## 194739 198164
## 1:241651974_C/T 1:242254442_G/A
## 199487 200526
## 1:242894159_T/C 10:277343_A/G
## 201192 208291
## 10:472607_ACT/A 10:1183069_G/A
## 208580 209640
## 10:1185028_C/T 10:1185195_C/T
## 209647 209649
## 10:1186724_T/G 10:1217136_C/T
## 209653 209706
## 10:1217303_C/T 10:1233656_G/A
## 209708 209730
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## 2376328 2378335
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## 2398568 2403510
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## 2418645 2424133
## 9:123485656_GCACACACA/G 9:124066361_T/C
## 2424182 2424579
## 9:136078052_A/G 9:136510909_A/G
## 2444162 2445108
## 9:136511049_A/G 9:136513000_C/T
## 2445109 2445114
## X:2668319_C/T X:71594286_C/T
## 2454926 2482978
## X:151226481_T/C X:151227838_TC/T
## 2512589 2512593
## X:152650860_G/A X:153448079_C/A
## 2513260 2513714
## X:153550428_C/T X:155451167_C/T
## 2513850 2514986
## KI270728.1:1561554_A/G
## 2518147which( names(pred) %in% names(vars) )## [1] 1498 3608 5482 5503 15628 15632 22297 23473 23475 24096 30210 31900
## [13] 32874 35913 36275 36679 36685 40424 41073 42204 44443 44444 45213 46168
## [25] 50548 50549 50550df1 <- data.frame(pred[which( names(pred) %in% names(vars) )])
df1## seqnames start end width strand paramRangeID REF ALT QUAL FILTER
## 1 1 36286832 36286832 1 + <NA> C T 45.69 PASS
## 2 1 160166560 160166560 1 + <NA> G A 45.33 PASS
## 3 10 277343 277343 1 - <NA> A G 51.82 PASS
## 4 10 1185028 1185028 1 - <NA> C T 43.55 PASS
## 5 14 64779905 64779905 1 - <NA> T C 49.85 PASS
## 6 14 64786514 64786514 1 - <NA> T C 54.12 PASS
## 7 17 47808390 47808390 1 - <NA> C T 57.19 PASS
## 8 17 81941396 81941396 1 - <NA> A G 49.33 PASS
## 9 17 81941619 81941619 1 - <NA> G A 48.49 PASS
## 10 18 50806833 50806833 1 - <NA> C G 48.85 PASS
## 11 2 74886530 74886530 1 + <NA> C T 50.38 PASS
## 12 2 207946373 207946373 1 - <NA> C T 50.84 PASS
## 13 20 1118880 1118880 1 + <NA> T G 49.44 PASS
## 14 22 43580516 43580516 1 - <NA> G A 48.22 PASS
## 15 3 4362153 4362153 1 - <NA> A G 47.08 PASS
## 16 3 38477933 38477933 1 + <NA> A G 48.94 PASS
## 17 3 38580976 38580976 1 - <NA> T C 52.11 PASS
## 18 4 129109497 129109497 1 + <NA> A G 43.26 PASS
## 19 5 10624775 10624775 1 + <NA> T C 52.12 PASS
## 20 5 139478334 139478334 1 - <NA> T C 51.65 PASS
## 21 6 32443258 32443258 1 + <NA> A C 50.43 PASS
## 22 6 32443869 32443869 1 + <NA> T G 47.92 PASS
## 23 6 53654264 53654264 1 - <NA> A G 45.36 PASS
## 24 6 152143704 152143704 1 - <NA> A G 50.28 PASS
## 25 8 140549259 140549259 1 - <NA> G A 48.82 PASS
## 26 8 140556212 140556212 1 - <NA> C T 50.72 PASS
## 27 8 140558523 140558523 1 - <NA> G A 48.95 PASS
## varAllele CDSLOC.start CDSLOC.end CDSLOC.width PROTEINLOC QUERYID TXID
## 1 T 602 602 1 201 49990 2622
## 2 A 1080 1080 1 360 130129 7899
## 3 C 4596 4596 1 1532 208291 126639
## 4 A 1876 1876 1 626 209647 126673
## 5 G 4293 4293 1 1431 687704 171301
## 6 G 3451 3451 1 1151 687728 171301
## 7 A 2430 2430 1 810 961722 205442
## 8 C 346 346 1 116 1003309 208245
## 9 T 123 123 1 41 1003311 208245
## 10 C 117 117 1 39 1042870 212444
## 11 T 2076 2076 1 692 1231933 25352
## 12 A 1686 1686 1 562 1322290 39796
## 13 G 107 107 1 36 1358686 227584
## 14 T 2720 2720 1 907 1501462 241778
## 15 C 1116 1116 1 372 1519329 49432
## 16 G 333 333 1 111 1546499 42900
## 17 G 3183 3183 1 1061 1546614 50615
## 18 G 319 319 1 107 1760186 60780
## 19 C 547 547 1 183 1816864 67647
## 20 G 695 695 1 232 1897631 77379
## 21 C 402 402 1 134 1975249 81122
## 22 G 649 649 1 217 1975255 81121
## 23 C 1009 1009 1 337 2000438 87543
## 24 C 1572 1572 1 524 2061133 90352
## 25 T 1443 1443 1 481 2332564 112703
## 26 A 1101 1101 1 367 2332581 112703
## 27 T 840 840 1 280 2332587 112703
## CDSID GENEID CONSEQUENCE REFCODON VARCODON REFAA VARAA
## 1 3317 ENSG00000054118 nonsynonymous GCC GTC A V
## 2 9222 ENSG00000132681 synonymous GCG GCA A A
## 3 138097 ENSG00000151240 synonymous TAT TAC Y Y
## 4 138187 ENSG00000185736 nonsynonymous GCC ACC A T
## 5 187655 ENSG00000070182 synonymous CGA CGG R R
## 6 187661 ENSG00000070182 nonsynonymous AAT GAT N D
## 7 227172 ENSG00000006025 synonymous ACG ACA T T
## 8 230440 ENSG00000185105 nonsynonymous TCC CCC S P
## 9 230440 ENSG00000185105 synonymous GCC GCT A A
## 10 234576, .... ENSG00000134042 nonsynonymous AGG AGC R S
## 11 30016 ENSG00000159399 synonymous AAC AAT N N
## 12 45692 ENSG00000178385 synonymous AAG AAA K K
## 13 252934 ENSG00000125818 nonsynonymous TTC TGC F C
## 14 267188 ENSG00000186976 nonsynonymous GCT GTT A V
## 15 55655 ENSG00000144455 synonymous ACT ACC T T
## 16 49239 ENSG00000114739 synonymous GAA GAG E E
## 17 56827 ENSG00000183873 synonymous GAA GAG E E
## 18 68076, 6.... ENSG00000151470 nonsynonymous ATG GTG M V
## 19 74880 ENSG00000164236 nonsynonymous TCT CCT S P
## 20 84536 ENSG00000184584 nonsynonymous CAT CGT H R
## 21 88152 ENSG00000204287 synonymous ATA ATC I I
## 22 88154 ENSG00000204287 nonsynonymous TTG GTG L V
## 23 95939 ENSG00000124743 synonymous TTG CTG L L
## 24 98924 ENSG00000131018 synonymous CGT CGC R R
## 25 121217 ENSG00000123908 synonymous GCC GCT A A
## 26 121220 ENSG00000123908 synonymous GCG GCA A A
## 27 121222 ENSG00000123908 synonymous CGC CGT R Rdf2 <- data.frame(pred2[which( names(pred2) %in% names(vars) )])
df2## seqnames start end width strand paramRangeID REF ALT QUAL FILTER
## 1 1 36286832 36286832 1 + <NA> C T 45.69 PASS
## 2 10 1185028 1185028 1 - <NA> C T 43.55 PASS
## 3 14 64786514 64786514 1 - <NA> T C 54.12 PASS
## 4 17 81941396 81941396 1 - <NA> A G 49.33 PASS
## 5 18 50806833 50806833 1 - <NA> C G 48.85 PASS
## 6 20 1118880 1118880 1 + <NA> T G 49.44 PASS
## 7 22 43580516 43580516 1 - <NA> G A 48.22 PASS
## 8 4 129109497 129109497 1 + <NA> A G 43.26 PASS
## 9 5 10624775 10624775 1 + <NA> T C 52.12 PASS
## 10 5 139478334 139478334 1 - <NA> T C 51.65 PASS
## 11 6 32443869 32443869 1 + <NA> T G 47.92 PASS
## varAllele CDSLOC.start CDSLOC.end CDSLOC.width PROTEINLOC QUERYID TXID
## 1 T 602 602 1 201 49990 2622
## 2 A 1876 1876 1 626 209647 126673
## 3 G 3451 3451 1 1151 687728 171301
## 4 C 346 346 1 116 1003309 208245
## 5 C 117 117 1 39 1042870 212444
## 6 G 107 107 1 36 1358686 227584
## 7 T 2720 2720 1 907 1501462 241778
## 8 G 319 319 1 107 1760186 60780
## 9 C 547 547 1 183 1816864 67647
## 10 G 695 695 1 232 1897631 77379
## 11 G 649 649 1 217 1975255 81121
## CDSID GENEID CONSEQUENCE REFCODON VARCODON REFAA VARAA
## 1 3317 ENSG00000054118 nonsynonymous GCC GTC A V
## 2 138187 ENSG00000185736 nonsynonymous GCC ACC A T
## 3 187661 ENSG00000070182 nonsynonymous AAT GAT N D
## 4 230440 ENSG00000185105 nonsynonymous TCC CCC S P
## 5 234576, .... ENSG00000134042 nonsynonymous AGG AGC R S
## 6 252934 ENSG00000125818 nonsynonymous TTC TGC F C
## 7 267188 ENSG00000186976 nonsynonymous GCT GTT A V
## 8 68076, 6.... ENSG00000151470 nonsynonymous ATG GTG M V
## 9 74880 ENSG00000164236 nonsynonymous TCT CCT S P
## 10 84536 ENSG00000184584 nonsynonymous CAT CGT H R
## 11 88154 ENSG00000204287 nonsynonymous TTG GTG L Vvars2 <- pred2[which( names(pred2) %in% names(vars) )]
#> snpsByOverlaps(snps, "22:33.63e6-33.64e6")Another try. This time I’m only looking for homozygous variants in the affected individuals.
vars <- which(cnt_aff == max(cnt_aff) )
str(vars) ## Named int [1:22434] 60 179 249 258 259 276 378 379 394 415 ...
## - attr(*, "names")= chr [1:22434] "1:135982_A/G" "1:779047_G/A" "1:847924_T/C" "1:856883_A/G" ...pred2[which( names(pred2) %in% names(vars) )]## GRanges object with 1846 ranges and 17 metadata columns:
## seqnames ranges strand | paramRangeID
## <Rle> <IRanges> <Rle> | <factor>
## 1:942451_T/C 1 942451 + | NA
## 1:979496_T/C 1 979496 - | NA
## 1:1623412_T/C 1 1623412 + | NA
## 1:1668449_A/G 1 1668449 - | NA
## 1:3473163_C/T 1 3473163 + | NA
## ... ... ... ... . ...
## X:154465991_G/C X 154465991 + | NA
## X:154485448_T/C X 154485448 - | NA
## X:154653251_C/G X 154653251 - | NA
## X:154653499_C/T X 154653499 - | NA
## KI270734.1:150464_A/G KI270734.1 150464 - | NA
## REF ALT QUAL FILTER
## <DNAStringSet> <DNAStringSetList> <numeric> <character>
## 1:942451_T/C T C 36.91 PASS
## 1:979496_T/C T C 49.06 PASS
## 1:1623412_T/C T C 54.75 PASS
## 1:1668449_A/G A G 43.10 PASS
## 1:3473163_C/T C T 53.11 PASS
## ... ... ... ... ...
## X:154465991_G/C G C 55.58 PASS
## X:154485448_T/C T C 55.62 PASS
## X:154653251_C/G C G 48.14 PASS
## X:154653499_C/T C T 33.14 PASS
## KI270734.1:150464_A/G A G 20.48 PASS
## varAllele CDSLOC PROTEINLOC QUERYID
## <DNAStringSet> <IRanges> <IntegerList> <integer>
## 1:942451_T/C C 1516 506 426
## 1:979496_T/C G 1534 512 550
## 1:1623412_T/C C 134 45 1895
## 1:1668449_A/G C 610 204 1970
## 1:3473163_C/T T 1108 370 5007
## ... ... ... ... ...
## X:154465991_G/C C 2589 863 2514591
## X:154485448_T/C G 425 142 2514618
## X:154653251_C/G C 265 89 2514711
## X:154653499_C/T A 17 6 2514712
## KI270734.1:150464_A/G C 229 77 2522043
## TXID CDSID GENEID CONSEQUENCE
## <character> <IntegerList> <character> <factor>
## 1:942451_T/C 115 18 ENSG00000187634 nonsynonymous
## 1:979496_T/C 11712 13792,13791 ENSG00000187642 nonsynonymous
## 1:1623412_T/C 244 231,232 ENSG00000197530 nonsynonymous
## 1:1668449_A/G 11939 14074 ENSG00000189339 nonsynonymous
## 1:3473163_C/T 424 451 ENSG00000130762 nonsynonymous
## ... ... ... ... ...
## X:154465991_G/C 246179 272265 ENSG00000130827 nonsynonymous
## X:154485448_T/C 250046 276743 ENSG00000102178 nonsynonymous
## X:154653251_C/G 250110 276808 ENSG00000126890 nonsynonymous
## X:154653499_C/T 250110 276808 ENSG00000126890 nonsynonymous
## KI270734.1:150464_A/G 251118 277521 ENSG00000277196 nonsynonymous
## REFCODON VARCODON REFAA
## <DNAStringSet> <DNAStringSet> <AAStringSet>
## 1:942451_T/C TGG CGG W
## 1:979496_T/C AGC GGC S
## 1:1623412_T/C ATG ACG M
## 1:1668449_A/G TGG CGG W
## 1:3473163_C/T CAC TAC H
## ... ... ... ...
## X:154465991_G/C GAG GAC E
## X:154485448_T/C CAT CGT H
## X:154653251_C/G GAG CAG E
## X:154653499_C/T CGG CAG R
## KI270734.1:150464_A/G TGG CGG W
## VARAA
## <AAStringSet>
## 1:942451_T/C R
## 1:979496_T/C G
## 1:1623412_T/C T
## 1:1668449_A/G R
## 1:3473163_C/T Y
## ... ...
## X:154465991_G/C D
## X:154485448_T/C R
## X:154653251_C/G Q
## X:154653499_C/T Q
## KI270734.1:150464_A/G R
## -------
## seqinfo: 40 sequences from GRCh38 genomechrcnt <- table(sapply(strsplit(unique(names(pred2[which( names(pred2) %in% names(vars) )])),":"),"[[",1))
#chrcnt <- chrcnt[order(-chrcnt)]
chrcnt_ctrl <- table(seqnames(vcf))
chrcnt_ctrl <- chrcnt_ctrl[which(names(chrcnt_ctrl) %in% names(chrcnt))]
chrcnt_ctrl <- chrcnt_ctrl[order(names(chrcnt_ctrl))]
chrcnt_df <- data.frame(cbind(chrcnt,chrcnt_ctrl))
chrcnt_df$rate <- chrcnt_df$chrcnt / chrcnt_df$chrcnt_ctrl * 1000000
chrcnt_df[order(-chrcnt_df$rate),] ## chrcnt chrcnt_ctrl rate
## MT 3 103 29126.2136
## KI270734.1 1 55 18181.8182
## 11 165 118568 1391.6065
## 19 131 98891 1324.6908
## 17 105 102144 1027.9605
## 16 95 93210 1019.2039
## 12 118 119880 984.3177
## 1 184 208092 884.2243
## X 53 67174 788.9957
## 3 111 147895 750.5325
## 6 109 145280 750.2753
## 7 103 143284 718.8521
## 15 55 78928 696.8376
## 8 71 115744 613.4227
## 22 33 55079 599.1394
## 10 75 129509 579.1103
## 14 46 80292 572.9089
## 5 74 132733 557.5102
## 18 33 61626 535.4883
## 9 56 107480 521.0272
## 20 34 66487 511.3782
## 2 94 190390 493.7234
## 4 61 140036 435.6023
## 21 15 36909 406.4049
## 13 21 75601 277.7741candidates <- unique(names(pred2[which( names(pred2) %in% names(vars) )]))It appears that there are three non-synonymous variants on the mtDNA.
candidates[grep("MT",candidates)]## [1] "MT:4769_A/G" "MT:8860_A/G" "MT:15326_A/G"pred[names(pred) %in% candidates[grep("MT",candidates)]]## GRanges object with 3 ranges and 17 metadata columns:
## seqnames ranges strand | paramRangeID REF
## <Rle> <IRanges> <Rle> | <factor> <DNAStringSet>
## MT:4769_A/G MT 4769 + | NA A
## MT:8860_A/G MT 8860 + | NA A
## MT:15326_A/G MT 15326 + | NA A
## ALT QUAL FILTER varAllele
## <DNAStringSetList> <numeric> <character> <DNAStringSet>
## MT:4769_A/G G 33.87 PASS G
## MT:8860_A/G G 41.22 PASS G
## MT:15326_A/G G 41.49 PASS G
## CDSLOC PROTEINLOC QUERYID TXID CDSID
## <IRanges> <IntegerList> <integer> <character> <IntegerList>
## MT:4769_A/G 300 100 2448087 251034 277406
## MT:8860_A/G 334 112 2448110 251041 277410
## MT:15326_A/G 580 194 2448143 251052 277416
## GENEID CONSEQUENCE REFCODON VARCODON
## <character> <factor> <DNAStringSet> <DNAStringSet>
## MT:4769_A/G ENSG00000198763 nonsynonymous ATA ATG
## MT:8860_A/G ENSG00000198899 nonsynonymous ACA GCA
## MT:15326_A/G ENSG00000198727 nonsynonymous ACA GCA
## REFAA VARAA
## <AAStringSet> <AAStringSet>
## MT:4769_A/G I M
## MT:8860_A/G T A
## MT:15326_A/G T A
## -------
## seqinfo: 40 sequences from GRCh38 genomeSession information
sessionInfo()## R version 4.0.1 (2020-06-06)
## Platform: x86_64-conda_cos6-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS/LAPACK: /ceph-g/opt/miniconda3/envs/R40/lib/libopenblasp-r0.3.9.so
##
## 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] SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20
## [2] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
## [3] GenomicFeatures_1.40.1
## [4] AnnotationDbi_1.50.3
## [5] SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20
## [6] BSgenome.Hsapiens.UCSC.hg38_1.4.3
## [7] BSgenome_1.56.0
## [8] VariantAnnotation_1.34.0
## [9] Rsamtools_2.4.0
## [10] SummarizedExperiment_1.18.2
## [11] DelayedArray_0.14.1
## [12] matrixStats_0.62.0
## [13] Biobase_2.48.0
## [14] eulerr_6.1.1
## [15] Biostrings_2.56.0
## [16] XVector_0.28.0
## [17] R.utils_2.12.0
## [18] R.oo_1.25.0
## [19] R.methodsS3_1.8.2
## [20] rtracklayer_1.48.0
## [21] GenomicRanges_1.40.0
## [22] GenomeInfoDb_1.24.2
## [23] IRanges_2.22.2
## [24] S4Vectors_0.26.1
## [25] BiocGenerics_0.34.0
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.1 bit64_4.0.5 assertthat_0.2.1
## [4] askpass_1.1 BiocManager_1.30.18 BiocFileCache_1.12.1
## [7] blob_1.2.1 GenomeInfoDbData_1.2.3 yaml_2.2.1
## [10] progress_1.2.2 pillar_1.8.0 RSQLite_2.2.15
## [13] lattice_0.20-41 glue_1.6.2 digest_0.6.25
## [16] htmltools_0.5.0 Matrix_1.2-18 XML_3.99-0.10
## [19] pkgconfig_2.0.3 biomaRt_2.44.4 zlibbioc_1.34.0
## [22] purrr_0.3.4 BiocParallel_1.22.0 tibble_3.0.1
## [25] openssl_1.4.1 generics_0.0.2 ellipsis_0.3.2
## [28] cachem_1.0.6 cli_3.3.0 magrittr_1.5
## [31] crayon_1.3.4 memoise_2.0.1 evaluate_0.14
## [34] fansi_0.4.1 xml2_1.3.2 tools_4.0.1
## [37] prettyunits_1.1.1 hms_0.5.3 lifecycle_1.0.1
## [40] stringr_1.4.0 compiler_4.0.1 rlang_1.0.4
## [43] grid_4.0.1 RCurl_1.98-1.8 rappdirs_0.3.3
## [46] tcltk_4.0.1 bitops_1.0-7 rmarkdown_2.3
## [49] DBI_1.1.0 curl_4.3 R6_2.4.1
## [52] GenomicAlignments_1.24.0 knitr_1.28 dplyr_1.0.9
## [55] fastmap_1.0.1 bit_4.0.4 utf8_1.1.4
## [58] stringi_1.4.6 Rcpp_1.0.9 vctrs_0.4.1
## [61] dbplyr_1.4.4 tidyselect_1.1.2 xfun_0.15