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example.vcf
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201 lines (201 loc) · 20.6 KB
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##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aln.sorted.bam
chr1 10439 . acccc accc 7.15 . INDEL;DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,0,2;MQ=29;FQ=-40.5 GT:PL:GQ 1/1:45,6,0:7
chr1 14907 . A G 24 . DP=50;VDB=0.0520;AF1=0.5;AC1=1;DP4=15,6,17,3;MQ=21;FQ=27;PV4=0.45,1.6e-22,0.18,0.0096 GT:PL:GQ 0/1:54,0,127:57
chr1 14930 . A G 96 . DP=69;VDB=0.0205;AF1=0.5;AC1=1;DP4=20,9,31,6;MQ=24;FQ=98.9;PV4=0.24,1.1e-25,1,1 GT:PL:GQ 0/1:126,0,143:99
chr1 15118 . A G 7 . DP=27;VDB=0.0345;AF1=0.5031;AC1=1;DP4=2,12,0,11;MQ=12;FQ=-8.7;PV4=0.49,1,1,1 GT:PL:GQ 0/1:36,0,19:24
chr1 15211 . T G 23.1 . DP=6;VDB=0.0262;AF1=1;AC1=2;DP4=0,2,1,3;MQ=20;FQ=-32;PV4=1,0.018,1,1 GT:PL:GQ 1/1:54,5,0:9
chr1 98889 . G T 6.98 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=36;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
chr1 120871 . C T 3.01 . DP=59;VDB=0.0345;AF1=1;AC1=2;DP4=15,32,11,0;MQ=13;FQ=-60;PV4=3.4e-05,1.2e-20,1,1 GT:PL:GQ 1/1:33,33,0:28
chr1 663097 . G C 19.5 . DP=7;VDB=0.0013;AF1=1;AC1=2;DP4=1,1,1,4;MQ=13;FQ=-34;PV4=1,0.0059,1,1 GT:PL:GQ 1/1:51,7,0:12
chr1 725751 . ct cTt 24.5 . INDEL;DP=3;VDB=0.0292;AF1=1;AC1=2;DP4=0,1,0,2;MQ=30;FQ=-37.5;PV4=1,1,1,0 GT:PL:GQ 1/1:62,3,0:6
chr1 752721 . A G 4.61 . DP=4;VDB=0.0057;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
chr1 753269 . C G 42 . DP=29;VDB=0.0504;AF1=1;AC1=2;DP4=0,0,12,16;MQ=10;FQ=-111 GT:PL:GQ 1/1:75,84,0:99
chr1 753405 . C A 31 . DP=9;VDB=0.0249;AF1=1;AC1=2;DP4=0,0,0,8;MQ=20;FQ=-51 GT:PL:GQ 1/1:64,24,0:44
chr10 93603 . C T 120 . DP=31;VDB=0.0345;AF1=1;AC1=2;DP4=1,0,13,6;MQ=23;FQ=-74;PV4=1,9.5e-07,1,1 GT:PL:GQ 1/1:153,47,0:91
chr10 93945 . G A 121 . DP=126;VDB=0.0523;AF1=0.5;AC1=1;DP4=5,29,20,62;MQ=27;FQ=36;PV4=0.32,2.1e-30,1,0.063 GT:PL:GQ 0/1:151,0,63:66
chr10 94018 . T C 6.98 . DP=54;VDB=0.0165;AF1=0.4999;AC1=1;DP4=12,27,1,10;MQ=33;FQ=9.53;PV4=0.25,1,0.12,1 GT:PL:GQ 0/1:36,0,244:37
chr10 94026 . G A 129 . DP=53;VDB=0.0436;AF1=0.5;AC1=1;DP4=2,11,12,23;MQ=30;FQ=46;PV4=0.29,3.1e-11,1,1 GT:PL:GQ 0/1:159,0,73:76
chr10 94083 . C T 64 . DP=27;VDB=0.0345;AF1=0.5032;AC1=1;DP4=1,7,4,13;MQ=17;FQ=-8.63;PV4=1,1,1,0.26 GT:PL:GQ 0/1:94,0,19:22
chr10 94136 . C T 87 . DP=14;VDB=0.0436;AF1=1;AC1=2;DP4=0,0,1,13;MQ=25;FQ=-69 GT:PL:GQ 1/1:120,42,0:81
chr10 94238 . A T 7.18 . DP=6;VDB=0.0013;AF1=1;AC1=2;DP4=0,0,0,5;MQ=12;FQ=-42 GT:PL:GQ 1/1:39,15,0:18
chr10 94426 . C T 35.5 . DP=4;VDB=0.0148;AF1=1;AC1=2;DP4=0,0,4,0;MQ=55;FQ=-39 GT:PL:GQ 1/1:68,12,0:21
chr10 94545 . C T 138 . DP=15;VDB=0.0520;AF1=1;AC1=2;DP4=0,0,6,8;MQ=50;FQ=-69 GT:PL:GQ 1/1:171,42,0:81
chr10 94870 . A G 6.79 . DP=3;VDB=0.0299;AF1=1;AC1=2;DP4=0,0,1,1;MQ=25;FQ=-33 GT:PL:GQ 1/1:37,6,0:7
chr11 178610 . G T 8.65 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=46;FQ=-30 GT:PL:GQ 1/1:38,3,0:5
chr11 180318 . C T 9.31 . DP=15;VDB=0.0297;AF1=1;AC1=2;DP4=3,4,0,5;MQ=13;FQ=-27;PV4=0.2,1.7e-06,1,1 GT:PL:GQ 0/1:37,0,0:4
chr11 190276 . A C 7.59 . DP=2;VDB=0.0166;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
chr11 190306 . A G 7.8 . DP=2;VDB=0.0166;AF1=1;AC1=2;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
chr11 190421 . C G 6.98 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=36;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
chr11 190571 . T C 3.98 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,2,0;MQ=31;FQ=-33 GT:PL:GQ 1/1:33,6,0:5
chr11 190727 . C T 6.02 . DP=2;VDB=0.0100;AF1=1;AC1=2;DP4=0,0,0,2;MQ=31;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
chr11 190729 . G A 7.59 . DP=2;VDB=0.0100;AF1=1;AC1=2;DP4=0,0,0,2;MQ=31;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
chr11 190761 . A G 36.8 . DP=2;VDB=0.0190;AF1=1;AC1=2;DP4=0,0,1,1;MQ=35;FQ=-33 GT:PL:GQ 1/1:68,6,0:10
chr11 193096 . T C 52 . DP=12;VDB=0.0392;AF1=0.5;AC1=1;DP4=2,1,4,1;MQ=54;FQ=32;PV4=1,0.06,1,0.15 GT:PL:GQ 0/1:82,0,59:62
chr12 82811 . G A 10.2 . DP=3;VDB=0.0135;AF1=1;AC1=2;DP4=0,0,2,0;MQ=47;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
chr12 83158 . ctcttt cTCTTtcttt 103 . INDEL;DP=3;VDB=0.0223;AF1=1;AC1=2;DP4=0,0,2,1;MQ=52;FQ=-43.5 GT:PL:GQ 1/1:143,9,0:16
chr12 83263 . C T 10.2 . DP=2;VDB=0.0184;AF1=1;AC1=2;DP4=0,0,0,2;MQ=47;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
chr12 84772 . T A 7.8 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
chr12 84856 . G T 25 . DP=3;VDB=0.0122;AF1=1;AC1=2;DP4=0,0,3,0;MQ=33;FQ=-36 GT:PL:GQ 1/1:57,9,0:15
chr12 84871 . G C 36.5 . DP=4;VDB=0.0295;AF1=1;AC1=2;DP4=0,0,4,0;MQ=40;FQ=-39 GT:PL:GQ 1/1:69,12,0:21
chr12 85105 . G A 47 . DP=22;VDB=0.0297;AF1=0.5;AC1=1;DP4=0,9,0,13;MQ=25;FQ=49.8;PV4=1,0.44,0.053,1 GT:PL:GQ 0/1:77,0,90:80
chr12 86381 . C G 12.3 . DP=13;VDB=0.0075;AF1=0.5;AC1=1;DP4=6,0,4,0;MQ=24;FQ=15.1;PV4=1,1,0.16,0.28 GT:PL:GQ 0/1:42,0,78:44
chr12 86386 . C T 39 . DP=14;VDB=0.0130;AF1=0.5;AC1=1;DP4=6,0,5,0;MQ=28;FQ=41.2;PV4=1,1,1,0.25 GT:PL:GQ 0/1:69,0,76:71
chr12 86886 . G C 30 . DP=11;VDB=0.0480;AF1=1;AC1=2;DP4=0,0,2,8;MQ=13;FQ=-57 GT:PL:GQ 1/1:63,30,0:54
chr13 19043558 . A C 154 . DP=58;VDB=0.0523;AF1=1;AC1=2;DP4=0,0,18,34;MQ=39;FQ=-184 GT:PL:GQ 1/1:187,157,0:99
chr13 19052437 . C A 14.9 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33 GT:PL:GQ 1/1:46,6,0:10
chr13 19058567 . T A 60.5 . DP=5;VDB=0.0055;AF1=1;AC1=2;DP4=0,0,4,0;MQ=37;FQ=-39 GT:PL:GQ 1/1:93,12,0:21
chr13 19059494 . C T 150 . DP=49;VDB=0.0345;AF1=0.5;AC1=1;DP4=9,3,21,15;MQ=25;FQ=58;PV4=0.49,0.038,1,1 GT:PL:GQ 0/1:180,0,85:88
chr13 19224587 . G A 4.77 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=41;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
chr13 19240208 . A G 72 . DP=9;VDB=0.0504;AF1=1;AC1=2;DP4=0,0,5,3;MQ=40;FQ=-51 GT:PL:GQ 1/1:105,24,0:45
chr13 19240438 . G C 11.4 . DP=5;VDB=0.0413;AF1=1;AC1=2;DP4=1,0,1,2;MQ=16;FQ=-32;PV4=1,0.074,1,0.21 GT:PL:GQ 1/1:42,5,0:8
chr13 19240484 . T C 39.1 . DP=7;VDB=0.0520;AF1=1;AC1=2;DP4=0,0,1,5;MQ=23;FQ=-45 GT:PL:GQ 1/1:72,18,0:33
chr13 19240668 . T C 32.8 . DP=8;VDB=0.0039;AF1=1;AC1=2;DP4=0,1,2,3;MQ=29;FQ=-37;PV4=1,0.0051,1,1 GT:PL:GQ 1/1:65,10,0:17
chr13 19254691 . C T 6.98 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=36;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
chr14 19039663 . T A 13.9 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
chr14 19067527 . C A 4.13 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=32;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
chr14 19085263 . T G 10.4 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chr14 19110239 . T C 24 . DP=33;VDB=0.0028;AF1=0.5;AC1=1;DP4=18,7,6,0;MQ=53;FQ=27;PV4=0.29,1,0.00014,1 GT:PL:GQ 0/1:54,0,255:57
chr14 19110263 . T C 74 . DP=45;VDB=0.0451;AF1=0.5;AC1=1;DP4=22,9,11,3;MQ=48;FQ=77;PV4=0.73,0.29,7.7e-07,0.013 GT:PL:GQ 0/1:104,0,255:99
chr14 19110349 . C T 12.3 . DP=29;VDB=0.0520;AF1=0.5;AC1=1;DP4=1,15,3,7;MQ=51;FQ=15.1;PV4=0.26,1.2e-10,3.1e-08,1 GT:PL:GQ 0/1:42,0,201:44
chr14 19110364 . C G 28 . DP=25;VDB=0.0436;AF1=0.5;AC1=1;DP4=1,13,2,6;MQ=48;FQ=31;PV4=0.53,0.00051,9.5e-06,1 GT:PL:GQ 0/1:58,0,180:61
chr14 19117262 . G A 128 . DP=89;VDB=0.0523;AF1=0.5;AC1=1;DP4=2,59,1,25;MQ=49;FQ=131;PV4=1,0.0024,1,0.12 GT:PL:GQ 0/1:158,0,235:99
chr14 19117980 . C G 33 . DP=37;VDB=0.0165;AF1=0.5;AC1=1;DP4=15,0,21,0;MQ=40;FQ=36;PV4=1,7.7e-20,0.12,0.18 GT:PL:GQ 0/1:63,0,158:66
chr14 19118067 . T C 70 . DP=131;VDB=0.0474;AF1=0.5;AC1=1;DP4=88,0,41,0;MQ=32;FQ=73;PV4=1,0.26,1,1 GT:PL:GQ 0/1:100,0,143:99
chr15 20020773 . A G 13.9 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,2,0;MQ=25;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
chr15 20020792 . C T 13 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,2,0;MQ=25;FQ=-33 GT:PL:GQ 1/1:44,6,0:9
chr15 20020854 . A T 13.9 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
chr15 20020859 . T G 13.9 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
chr15 20035539 . G C 8.44 . DP=2;VDB=0.0156;AF1=1;AC1=2;DP4=0,0,2,0;MQ=47;FQ=-33 GT:PL:GQ 1/1:39,6,0:8
chr15 20035554 . T C 12 . DP=3;VDB=0.0145;AF1=1;AC1=2;DP4=0,0,2,0;MQ=47;FQ=-33 GT:PL:GQ 1/1:43,6,0:9
chr15 20035560 . C A 10.2 . DP=2;VDB=0.0142;AF1=1;AC1=2;DP4=0,0,2,0;MQ=47;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
chr15 20035662 . A C 6.02 . DP=2;VDB=0.0201;AF1=1;AC1=2;DP4=0,0,0,2;MQ=47;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
chr15 20035696 . C G 4.61 . DP=2;VDB=0.0021;AF1=1;AC1=2;DP4=0,0,0,2;MQ=47;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
chr15 20046256 . attgtt att 21.5 . INDEL;DP=3;VDB=0.0298;AF1=0.5013;AC1=1;DP4=1,0,0,2;MQ=43;FQ=-11.8;PV4=0.33,1,0,1 GT:PL:GQ 0/1:59,0,23:26
chr16 64341 . GCC GCCC 14.4 . INDEL;DP=2;VDB=0.0256;AF1=1;AC1=2;DP4=0,0,2,0;MQ=29;FQ=-40.5 GT:PL:GQ 1/1:53,6,0:10
chr16 79811 . T C 54.3 . DP=5;VDB=0.0451;AF1=1;AC1=2;DP4=0,0,5,0;MQ=26;FQ=-42 GT:PL:GQ 1/1:87,15,0:27
chr16 81779 . G T 34 . DP=60;VDB=0.0436;AF1=0.5;AC1=1;DP4=37,6,10,3;MQ=33;FQ=37;PV4=0.42,5.1e-08,1,0.00073 GT:PL:GQ 0/1:64,0,198:67
chr16 83941 . G T 3.55 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
chr16 84170 . C T 104 . DP=7;VDB=0.0474;AF1=1;AC1=2;DP4=0,0,4,3;MQ=60;FQ=-48 GT:PL:GQ 1/1:137,21,0:39
chr16 84800 . C A 10.4 . DP=3;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chr16 84870 . C G 44.5 . DP=5;VDB=0.0267;AF1=1;AC1=2;DP4=0,0,2,2;MQ=54;FQ=-39 GT:PL:GQ 1/1:77,12,0:21
chr16 91867 . G T 12 . DP=2;VDB=0.0135;AF1=1;AC1=2;DP4=0,0,1,1;MQ=60;FQ=-33 GT:PL:GQ 1/1:43,6,0:9
chr16 96164 . G A 6.02 . DP=2;VDB=0.0125;AF1=1;AC1=2;DP4=0,0,1,1;MQ=60;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
chr16 101975 . A G 6.98 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=36;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
chr17 3936 . A G 41.8 . DP=2;VDB=0.0225;AF1=1;AC1=2;DP4=0,0,1,1;MQ=46;FQ=-33 GT:PL:GQ 1/1:73,6,0:10
chr17 4966 . A G 4.13 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
chr17 5522 . AGT AGTGT 22.5 . INDEL;DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-37.5 GT:PL:GQ 1/1:60,3,0:6
chr17 6115 . G C 11.1 . DP=3;VDB=0.0245;AF1=1;AC1=2;DP4=0,0,0,2;MQ=47;FQ=-33 GT:PL:GQ 1/1:42,6,0:9
chr17 11830 . A G 6.02 . DP=2;VDB=0.0180;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
chr17 13869 . T A 41 . DP=5;VDB=0.0175;AF1=0.5;AC1=1;DP4=2,0,3,0;MQ=60;FQ=19.1;PV4=1,1,1,0.21 GT:PL:GQ 0/1:71,0,46:49
chr17 13905 . G A 55.1 . DP=8;VDB=0.0345;AF1=1;AC1=2;DP4=0,0,6,0;MQ=47;FQ=-45 GT:PL:GQ 1/1:88,18,0:33
chr17 14008 . G C 111 . DP=9;VDB=0.0474;AF1=1;AC1=2;DP4=0,0,0,8;MQ=47;FQ=-51 GT:PL:GQ 1/1:144,24,0:45
chr17 15993 . C T 4.77 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
chr17 33865 . T C 4.13 . DP=2;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
chr18 12976 . C T 38 . DP=8;VDB=0.0105;AF1=0.5;AC1=1;DP4=0,4,2,1;MQ=57;FQ=41;PV4=0.14,0.073,0.14,0.004 GT:PL:GQ 0/1:68,0,101:71
chr18 13625 . G A 10.4 . DP=2;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chr18 48387 . G A 15.1 . DP=89;VDB=0.0504;AF1=0.5;AC1=1;DP4=19,37,9,15;MQ=25;FQ=18.1;PV4=0.8,0.2,0.0015,1 GT:PL:GQ 0/1:45,0,219:48
chr18 49125 . G T 28 . DP=4;VDB=0.0245;AF1=0.6672;AC1=1;DP4=1,0,0,3;MQ=31;FQ=-24;PV4=0.25,0.12,1,1 GT:PL:GQ 0/1:57,0,3:6
chr18 49147 . G A 49.8 . DP=6;VDB=0.0451;AF1=1;AC1=2;DP4=1,0,1,3;MQ=28;FQ=-27;PV4=0.4,0.27,1,0.25 GT:PL:GQ 0/1:78,0,0:3
chr18 73090 . C T 41.5 . DP=4;VDB=0.0442;AF1=1;AC1=2;DP4=0,0,2,2;MQ=47;FQ=-39 GT:PL:GQ 1/1:74,12,0:21
chr18 73380 . C T 10.2 . DP=2;VDB=0.0125;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
chr18 80500 . G T 6.2 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
chr18 84200 . C A 30 . DP=8;VDB=0.0474;AF1=0.5;AC1=1;DP4=0,2,0,5;MQ=44;FQ=21.7;PV4=1,5.9e-06,0.35,0.26 GT:PL:GQ 0/1:60,0,49:52
chr18 84841 . C T 32 . DP=4;VDB=0.0375;AF1=1;AC1=2;DP4=0,0,3,0;MQ=54;FQ=-36 GT:PL:GQ 1/1:64,9,0:16
chr19 105021 . G C 187 . DP=118;VDB=0.0345;AF1=0.5;AC1=1;DP4=57,29,21,9;MQ=48;FQ=190;PV4=0.82,1,1,1 GT:PL:GQ 0/1:217,0,255:99
chr19 240867 . A C 13 . DP=3;VDB=0.0298;AF1=1;AC1=2;DP4=0,0,1,1;MQ=33;FQ=-33 GT:PL:GQ 1/1:44,6,0:9
chr19 255406 . T C 3.55 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=33;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
chr19 274479 . G A 78 . DP=4;VDB=0.0436;AF1=1;AC1=2;DP4=0,0,2,1;MQ=60;FQ=-36 GT:PL:GQ 1/1:110,9,0:16
chr19 282753 . G A 222 . DP=31;VDB=0.0523;AF1=1;AC1=2;DP4=0,0,25,6;MQ=60;FQ=-120 GT:PL:GQ 1/1:255,93,0:99
chr19 287970 . G GT 96 . INDEL;DP=4;VDB=0.0025;AF1=1;AC1=2;DP4=0,0,2,2;MQ=54;FQ=-46.5 GT:PL:GQ 1/1:136,12,0:21
chr19 291334 . C A 6.2 . DP=8;VDB=0.0154;AF1=0.4999;AC1=1;DP4=1,3,0,2;MQ=60;FQ=8.65;PV4=1,0.32,1,1 GT:PL:GQ 0/1:35,0,95:36
chr19 294457 . T C 4.13 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
chr19 309230 . G A 9.31 . DP=2;VDB=0.0260;AF1=1;AC1=2;DP4=0,0,0,2;MQ=29;FQ=-33 GT:PL:GQ 1/1:40,6,0:8
chr19 312143 . T C 80.5 . DP=7;VDB=0.0523;AF1=1;AC1=2;DP4=0,0,4,0;MQ=54;FQ=-39 GT:PL:GQ 1/1:113,12,0:21
chr2 69431 . C T 10.4 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chr2 97707 . G T 6.2 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
chr2 122193 . G T 9.53 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:39,3,0:5
chr2 141324 . G T 10.4 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chr2 151666 . A C 5.46 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
chr2 154452 . G A 78.1 . DP=6;VDB=0.0100;AF1=1;AC1=2;DP4=0,0,2,4;MQ=54;FQ=-45 GT:PL:GQ 1/1:111,18,0:33
chr2 154556 . C G 83.5 . DP=4;VDB=0.0436;AF1=1;AC1=2;DP4=0,0,0,4;MQ=60;FQ=-39 GT:PL:GQ 1/1:116,12,0:21
chr2 163994 . G A 11.1 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33 GT:PL:GQ 1/1:42,6,0:9
chr2 166725 . A G 8.65 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 1/1:38,3,0:5
chr2 194039 . A G 10.4 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chr20 76962 . T C 222 . DP=94;VDB=0.0504;AF1=1;AC1=2;DP4=0,0,55,31;MQ=59;FQ=-282 GT:PL:GQ 1/1:255,255,0:99
chr20 126529 . G A 21.3 . DP=5;VDB=0.0382;AF1=1;AC1=2;DP4=0,0,0,5;MQ=60;FQ=-42 GT:PL:GQ 1/1:54,15,0:26
chr20 130796 . T C 4.77 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
chr20 134931 . T G 7.59 . DP=2;VDB=0.0135;AF1=1;AC1=2;DP4=0,0,1,1;MQ=60;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
chr20 138004 . G C 107 . DP=5;VDB=0.0436;AF1=1;AC1=2;DP4=0,0,5,0;MQ=60;FQ=-42 GT:PL:GQ 1/1:140,15,0:27
chr20 138178 . GCC GC 214 . INDEL;DP=37;VDB=0.0530;AF1=1;AC1=2;DP4=0,0,21,11;MQ=60;FQ=-131 GT:PL:GQ 1/1:255,96,0:99
chr20 139362 . G A 179 . DP=11;VDB=0.0474;AF1=1;AC1=2;DP4=0,0,9,1;MQ=60;FQ=-57 GT:PL:GQ 1/1:212,30,0:57
chr20 139745 . T C 54 . DP=14;VDB=0.0503;AF1=1;AC1=2;DP4=0,0,0,14;MQ=60;FQ=-69 GT:PL:GQ 1/1:87,42,0:81
chr20 161450 . G A 7.8 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
chr20 165908 . T C 37.8 . DP=2;VDB=0.0111;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33 GT:PL:GQ 1/1:69,6,0:10
chr21 9417712 . G A 10.2 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,0,2;MQ=29;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
chr21 9421140 . C T 7.8 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
chr21 9432291 . G T 6.02 . DP=2;VDB=0.0177;AF1=1;AC1=2;DP4=0,0,2,0;MQ=38;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
chr21 9434062 . T C 3.55 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
chr21 9473396 . T A 6.02 . DP=2;VDB=0.0187;AF1=1;AC1=2;DP4=0,0,2,0;MQ=47;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
chr21 9473537 . aggg agg 11.8 . INDEL;DP=4;VDB=0.0443;AF1=1;AC1=2;DP4=1,0,1,1;MQ=37;FQ=-37.5;PV4=1,0,1,1 GT:PL:GQ 1/1:49,3,0:5
chr21 9582726 . C T 3.55 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=57;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
chr21 9590334 . C A 222 . DP=100;VDB=0.0520;AF1=1;AC1=2;DP4=0,0,44,44;MQ=35;FQ=-282 GT:PL:GQ 1/1:255,255,0:99
chr21 9590475 . A C 50 . DP=28;VDB=0.0474;AF1=0.5;AC1=1;DP4=0,12,0,15;MQ=27;FQ=53;PV4=1,1.5e-16,1,0.23 GT:PL:GQ 0/1:80,0,102:83
chr21 9646773 . C G 10.4 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chr22 16152227 . G A 8.65 . DP=2;VDB=0.0187;AF1=1;AC1=2;DP4=0,0,1,0;MQ=43;FQ=-30 GT:PL:GQ 1/1:38,3,0:5
chr22 16159060 . G A 108 . DP=98;VDB=0.0436;AF1=1;AC1=2;DP4=2,31,8,53;MQ=29;FQ=-54;PV4=0.49,4.6e-32,1,1 GT:PL:GQ 1/1:141,27,0:51
chr22 16159158 . A G 76.1 . DP=9;VDB=0.0165;AF1=1;AC1=2;DP4=0,0,0,7;MQ=29;FQ=-48 GT:PL:GQ 1/1:109,21,0:39
chr22 16211376 . T C 6.98 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=40;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
chr22 16248258 . T C 3.54 . DP=2;AF1=0.5;AC1=1;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
chr22 16255188 . T C 86 . DP=12;VDB=0.0520;AF1=1;AC1=2;DP4=0,0,12,0;MQ=29;FQ=-63 GT:PL:GQ 1/1:119,36,0:69
chr22 16255517 . T C 102 . DP=31;VDB=0.0503;AF1=1;AC1=2;DP4=0,0,0,30;MQ=29;FQ=-117 GT:PL:GQ 1/1:135,90,0:99
chr22 16255891 . G A 78 . DP=66;VDB=0.0130;AF1=0.5;AC1=1;DP4=17,17,9,18;MQ=20;FQ=81;PV4=0.21,0.099,0.23,1 GT:PL:GQ 0/1:108,0,181:99
chr22 16256822 . C T 6.98 . DP=20;VDB=0.0532;AF1=1;AC1=2;DP4=0,6,0,14;MQ=12;FQ=-30;PV4=1,3.3e-18,1,0.019 GT:PL:GQ 1/1:36,3,0:4
chr22 16269779 . A G 48 . DP=25;VDB=0.0003;AF1=1;AC1=2;DP4=0,0,18,1;MQ=21;FQ=-84 GT:PL:GQ 1/1:81,57,0:99
chrX 302139 . G C 5.45 . DP=25;VDB=0.0532;AF1=1;AC1=2;DP4=0,0,3,20;MQ=0;FQ=-96 GT:PL:GQ 1/1:37,69,0:45
chrX 1407796 . CAT C 7.34 . INDEL;DP=34;VDB=0.0520;AF1=1;AC1=2;DP4=0,0,5,27;MQ=0;FQ=-131 GT:PL:GQ 1/1:47,96,0:60
chrX 2699968 . A G 30 . DP=3;VDB=0.0245;AF1=1;AC1=2;DP4=0,0,3,0;MQ=60;FQ=-36 GT:PL:GQ 1/1:62,9,0:16
chrX 2700027 . T C 83 . DP=11;VDB=0.0205;AF1=1;AC1=2;DP4=0,0,11,0;MQ=60;FQ=-60 GT:PL:GQ 1/1:116,33,0:63
chrX 2701355 . CAaaaaa CAAaaaaa 10.4 . INDEL;DP=4;VDB=0.0274;AF1=1;AC1=2;DP4=0,0,4,0;MQ=60;FQ=-46.5 GT:PL:GQ 1/1:50,12,0:17
chrX 2724760 . T C 131 . DP=15;VDB=0.0532;AF1=1;AC1=2;DP4=0,0,5,10;MQ=57;FQ=-72 GT:PL:GQ 1/1:164,45,0:87
chrX 2725036 . c cAT 81.2 . INDEL;DP=2;VDB=0.0246;AF1=1;AC1=2;DP4=0,0,1,1;MQ=60;FQ=-40.5 GT:PL:GQ 1/1:120,6,0:10
chrX 2725174 . ctgtg cTGtgtg 22.5 . INDEL;DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-37.5 GT:PL:GQ 1/1:60,3,0:6
chrX 2726396 . A G 17.1 . DP=3;VDB=0.0290;AF1=1;AC1=2;DP4=0,0,0,3;MQ=60;FQ=-36 GT:PL:GQ 1/1:49,9,0:15
chrX 2729156 . CTTTTTTTTT CTTTTTTTT 10.8 . INDEL;DP=10;VDB=0.0504;AF1=1;AC1=2;DP4=0,0,9,1;MQ=60;FQ=-64.5 GT:PL:GQ 1/1:51,30,0:37
chrY 2655281 . C A 19.1 . DP=7;VDB=0.0132;AF1=0.5;AC1=1;DP4=4,1,2,0;MQ=60;FQ=22;PV4=1,1,1,1 GT:PL:GQ 0/1:49,0,136:52
chrY 3527677 . G T 36.5 . DP=4;VDB=0.0002;AF1=1;AC1=2;DP4=0,0,4,0;MQ=23;FQ=-39 GT:PL:GQ 1/1:69,12,0:21
chrY 3718943 . G T 10.4 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chrY 4734731 . G T 10.4 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 1/1:40,3,0:5
chrY 5139682 . G T 6.98 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
chrY 5206554 . G T 21 . DP=7;VDB=0.0132;AF1=0.5;AC1=1;DP4=1,4,0,2;MQ=60;FQ=24;PV4=1,1,1,1 GT:PL:GQ 0/1:51,0,136:54
chrY 5218322 . G T 24 . DP=3;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,3,0;MQ=29;FQ=-36 GT:PL:GQ 1/1:56,9,0:15
chrY 5980259 . G T 4.61 . DP=2;VDB=0.0132;AF1=1;AC1=2;DP4=0,0,2,0;MQ=19;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
chrY 6428752 . G T 4.77 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
chrY 6444200 . T C 3.55 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
chrY 6668746 . A G 4.77 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
chrY 6738206 . G T 19.1 . DP=7;VDB=0.0132;AF1=0.5;AC1=1;DP4=0,5,0,2;MQ=57;FQ=22;PV4=1,0.12,1,0.33 GT:PL:GQ 0/1:49,0,119:52