77 lines
9.5 KiB
Plaintext
77 lines
9.5 KiB
Plaintext
##fileformat=VCFv4.1
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##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
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##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
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##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
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##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
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##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
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##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
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##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
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##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1 1148100 rs34108055 G A,C 469.32 . AC=1,3;AF=0.0033,0.0099;AN=304;DB;DP=1245;Dels=0.00;InbreedingCoeff=0.0182;MQ=59.11;MQ0=1;QD=13.80
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1 1888193 rs3820011 C A,T 29693.64 . AC=101,1;AF=0.3301,0.0033;AN=306;DB;DP=3501;Dels=0.00;InbreedingCoeff=-0.1164;MQ=59.27;MQ0=0;QD=15.70
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1 3662208 . G A,T 614.93 . AC=5,3;AF=0.0163,0.0098;AN=306;DP=1545;Dels=0.00;InbreedingCoeff=0.0182;MQ=59.21;MQ0=0;QD=9.18
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1 12439694 rs41300104 C A,G 548.41 . AC=1,1;AF=0.0033,0.0033;AN=306;DB;DP=4057;Dels=0.00;InbreedingCoeff=0.0033;MQ=59.43;MQ0=0;QD=12.46
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1 12837634 rs848578 T A,C 477571.20 . AC=242,2;AF=0.7908,0.0065;AN=306;DB;DP=18200;DS;Dels=0.00;InbreedingCoeff=-0.0281;MQ=58.19;MQ0=6;QD=26.94
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1 19597289 . C G,T 11174.95 . AC=6,14;AF=0.0196,0.0458;AN=306;DP=6465;Dels=0.00;InbreedingCoeff=-0.0088;MQ=57.16;MQ0=7;QD=13.75
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1 22986015 . C A,T 1006.38 . AC=2,1;AF=0.0065,0.0033;AN=306;DP=8030;Dels=0.00;InbreedingCoeff=-0.0000;MQ=58.99;MQ0=0;QD=9.96
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1 24122986 rs760941 C G,T 80069.62 . AC=1,160;AF=0.0033,0.5229;AN=306;DB;DP=7723;Dels=0.00;InbreedingCoeff=-0.0487;MQ=59.09;MQ0=1;QD=13.83
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1 27676289 . G C,T 726.57 . AC=9,9;AF=0.0294,0.0294;AN=306;DP=792;Dels=0.00;InbreedingCoeff=0.1229;MQ=58.84;MQ0=0;QD=9.69
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1 32136168 rs2292990 G C,T 7842.61 . AC=125,58;AF=0.6068,0.2816;AN=206;DB;DP=318;Dels=0.00;InbreedingCoeff=0.6394;MQ=58.49;MQ0=0;QD=26.41
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1 32681070 rs11590013 C A,T 1585.55 . AC=1,2;AF=0.0033,0.0065;AN=306;DB;DP=8801;Dels=0.00;InbreedingCoeff=-0.0000;MQ=59.53;MQ0=0;QD=12.39
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1 37356469 rs511852 G A,C 5178.44 . AC=3,3;AF=0.0098,0.0098;AN=306;DB;DP=7593;Dels=0.00;InbreedingCoeff=0.6699;MQ=59.50;MQ0=0;QD=20.31
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1 40879808 rs209605 G C,T 171035.83 . AC=18,259;AF=0.0588,0.8464;AN=306;DB;DP=5668;Dels=0.00;InbreedingCoeff=0.0928;MQ=59.51;MQ0=0;QD=30.43
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1 42048869 . G C,T 1223.07 . AC=1,1;AF=0.0033,0.0033;AN=306;DP=10365;Dels=0.00;InbreedingCoeff=0.0033;MQ=58.86;MQ0=0;QD=9.20
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1 48697781 rs12161316 C A,T 3133.21 . AC=2,2;AF=0.0065,0.0065;AN=306;DB;DP=8265;Dels=0.00;InbreedingCoeff=0.0065;MQ=59.29;MQ0=0;QD=12.48
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1 67561056 rs61782288 C G,T 9937.98 . AC=3,30;AF=0.0098,0.0980;AN=306;DB;DP=4031;Dels=0.00;InbreedingCoeff=-0.0163;MQ=59.56;MQ0=0;QD=13.54
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1 68943442 rs3790476 A C,G 138834.72 . AC=2,165;AF=0.0065,0.5392;AN=306;DB;DP=8369;Dels=0.00;InbreedingCoeff=-0.1445;MQ=59.49;MQ0=0;QD=20.08
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1 89655681 . C A,T 12753.17 . AC=9,13;AF=0.0294,0.0425;AN=306;DP=6729;Dels=0.00;InbreedingCoeff=0.0179;MQ=59.35;MQ0=0;QD=14.15
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1 111773830 rs2147789 A C,T 62636.11 . AC=2,125;AF=0.0065,0.4085;AN=306;DB;DP=5119;Dels=0.00;InbreedingCoeff=-0.0263;MQ=59.60;MQ0=0;QD=18.88
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1 111783982 rs13721 C A,T 189791.24 . AC=98,45;AF=0.3203,0.1471;AN=306;DB;DP=13560;Dels=0.00;InbreedingCoeff=0.2554;MQ=59.43;MQ0=1;QD=19.82
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1 115399884 rs17544210 C G,T 11480.97 . AC=20,3;AF=0.0654,0.0098;AN=306;DB;DP=7703;Dels=0.00;InbreedingCoeff=0.0546;MQ=58.27;MQ0=0;QD=11.80
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1 118165691 rs1630312 C G,T 130574.99 . AC=17,90;AF=0.0556,0.2941;AN=306;DB;DP=12629;Dels=0.00;InbreedingCoeff=0.1310;MQ=59.59;MQ0=1;QD=18.81
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1 118490987 . C A,G 727.35 . AC=1,3;AF=0.0033,0.0098;AN=306;DP=2844;Dels=0.00;InbreedingCoeff=-0.0025;MQ=59.47;MQ0=0;QD=10.24
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1 118497292 rs2295631 G A,T 11389.76 . AC=5,4;AF=0.0163,0.0131;AN=306;DB;DP=12107;Dels=0.00;InbreedingCoeff=0.0129;MQ=59.76;MQ0=0;QD=18.92
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1 119923724 rs2275607 T C,G 483546.66 . AC=164,1;AF=0.5359,0.0033;AN=306;DB;DP=28081;DS;Dels=0.00;InbreedingCoeff=0.0529;MQ=59.67;MQ0=0;QD=22.42
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1 146714392 rs1890042 G C,T 12868.17 . AC=185,65;AF=0.6560,0.2305;AN=282;DB;DP=482;Dels=0.00;InbreedingCoeff=0.4658;MQ=59.23;MQ0=0;QD=27.79
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1 150130983 rs34773647 G C,T 57100.60 . AC=10,48;AF=0.0327,0.1569;AN=306;DB;DP=15263;Dels=0.00;InbreedingCoeff=-0.1054;MQ=60.03;MQ0=0;QD=10.54
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1 150130983 rs34875891 G GT,GCT 91690.78 . AC=66,3;AF=0.2157,0.0098;AN=306;BaseQRankSum=72.690;DB;DP=15164;FS=18.693;HaplotypeScore=351.4814;InbreedingCoeff=0.2172;MQ=60.03;MQ0=0;MQRankSum=25.710;QD=17.01;ReadPosRankSum=0.374
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1 150477088 . C G,T 7734.78 . AC=1,2;AF=0.0033,0.0065;AN=306;DP=29145;DS;Dels=0.00;InbreedingCoeff=-0.0000;MQ=59.73;MQ0=2;QD=11.92
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1 154744807 rs1051614 C G,T 90009.17 . AC=178,6;AF=0.5817,0.0196;AN=306;DB;DP=4622;Dels=0.00;InbreedingCoeff=0.0099;MQ=59.35;MQ0=0;QD=23.23
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1 155160270 rs1611770 C A,T 576.62 . AC=1,2;AF=0.0033,0.0065;AN=306;DB;DP=4575;Dels=0.00;InbreedingCoeff=-0.0000;MQ=59.19;MQ0=0;QD=10.88
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1 156533433 . G A,T 1544.92 . AC=2,5;AF=0.0065,0.0163;AN=306;DP=3099;Dels=0.00;InbreedingCoeff=-0.0034;MQ=59.36;MQ0=0;QD=13.67
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1 156706559 rs8658 A C,G 167288.91 . AC=109,197;AF=0.3562,0.6438;AN=306;DB;DP=4567;Dels=0.00;InbreedingCoeff=0.5686;MQ=59.44;MQ0=0;QD=36.63
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1 156708244 rs28697076 C G,T 177579.76 . AC=9,56;AF=0.0294,0.1830;AN=306;DB;DP=24764;DS;Dels=0.00;InbreedingCoeff=0.1419;MQ=59.61;MQ0=0;QD=18.38
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1 168059866 rs275149 A C,G 23982.90 . AC=108,59;AF=0.3553,0.1941;AN=304;DB;DP=3978;Dels=0.02;InbreedingCoeff=-0.0331;MQ=59.08;MQ0=0;QD=6.67
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1 169941761 rs511443 A C,T 57998.99 . AC=1,280;AF=0.0033,0.9150;AN=306;DB;DP=1920;Dels=0.00;InbreedingCoeff=-0.0786;MQ=59.46;MQ0=0;QD=30.21
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1 171162438 rs28969551 C A,T 28047.04 . AC=1,27;AF=0.0033,0.0882;AN=306;DB;DP=11499;Dels=0.00;InbreedingCoeff=-0.0903;MQ=59.25;MQ0=0;QD=13.07
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1 181018180 rs2236411 C A,G 25391.03 . AC=1,29;AF=0.0033,0.0948;AN=306;DB;DP=11674;Dels=0.00;InbreedingCoeff=-0.0225;MQ=36.45;MQ0=1103;QD=10.85
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1 202104616 rs61758714 T A,C 9963.64 . AC=3,1;AF=0.0098,0.0033;AN=306;DB;DP=31120;DS;Dels=0.00;InbreedingCoeff=-0.0034;MQ=59.63;MQ0=0;QD=11.08
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1 204234222 rs4076020 T A,C 148764 . AC=2,208;AF=0.0065,0.6797;AN=306;DB;DP=7509;Dels=0.00;InbreedingCoeff=0.1664;MQ=58.40;MQ0=0;QD=23.21
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1 207642050 rs61759494 C A,G 10338.77 . AC=2,2;AF=0.0065,0.0065;AN=306;DB;DP=30089;DS;Dels=0.00;InbreedingCoeff=0.0065;MQ=59.63;MQ0=0;QD=14.40
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1 208270244 rs3818517 A C,T 26388.22 . AC=95,1;AF=0.3105,0.0033;AN=306;DB;DP=3268;Dels=0.00;InbreedingCoeff=0.0678;MQ=59.25;MQ0=0;QD=16.63
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1 211280737 . A C,G 5650.08 . AC=22,4;AF=0.0719,0.0131;AN=306;DP=11279;Dels=0.00;InbreedingCoeff=-0.0511;MQ=59.88;MQ0=0;QD=3.28
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1 211280737 . AAG A 16872.42 . AC=23;AF=0.0752;AN=306;BaseQRankSum=-12.328;DP=11141;FS=542.007;HRun=0;HaplotypeScore=323.9945;InbreedingCoeff=-0.0813;MQ=59.95;MQ0=0;MQRankSum=6.655;QD=11.24;ReadPosRankSum=-15.661
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1 214813782 rs3795524 A C,G 16590.58 . AC=1,11;AF=0.0033,0.0359;AN=306;DB;DP=11758;Dels=0.00;InbreedingCoeff=-0.0308;MQ=59.51;MQ0=0;QD=15.92
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1 228494382 rs1150911 T C,G 37788.01 . AC=65,148;AF=0.2124,0.4837;AN=306;DB;DP=1640;Dels=0.00;InbreedingCoeff=0.3178;MQ=58.88;MQ0=0;QD=25.24
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1 236702374 rs2472126 G A,C 244521.93 . AC=200,12;AF=0.6536,0.0392;AN=306;DB;DP=12001;Dels=0.00;InbreedingCoeff=0.0166;MQ=58.65;MQ0=0;QD=22.33
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1 236902560 rs7527525 C G,T 215057.79 . AC=23,183;AF=0.0752,0.5980;AN=306;DB;DP=11941;Dels=0.00;InbreedingCoeff=0.1337;MQ=59.02;MQ0=1;QD=20.07
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1 241964559 rs4658661 C G,T 114843.77 . AC=42,153;AF=0.1373,0.5000;AN=306;DB;DP=5331;Dels=0.00;InbreedingCoeff=0.3029;MQ=59.66;MQ0=0;QD=25.27
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2 1842968 rs6728368 T A,C 45146.15 . AC=13,108;AF=0.0425,0.3529;AN=306;DB;DP=4138;Dels=0.00;InbreedingCoeff=0.0689;MQ=59.31;MQ0=0;QD=17.53
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2 1926488 rs13399855 C A,T 6170.25 . AC=1,10;AF=0.0033,0.0327;AN=306;DB;DP=7613;Dels=0.00;InbreedingCoeff=-0.0273;MQ=59.45;MQ0=0;QD=13.02
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2 10051053 rs10495576 G A,C 187513.81 . AC=4,201;AF=0.0131,0.6569;AN=306;DB;DP=8380;Dels=0.00;InbreedingCoeff=0.0820;MQ=59.67;MQ0=0;QD=25.60
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