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##fileformat=VCFv4.1
##samtoolsVersion=0.1.18-r572
##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=DV,Number=1,Type=Integer,Description="# high-quality non-reference 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">
##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
##FILTER=<ID=MaxDP,Description="Maximum read depth (INFO/DP or INFO/DP4) [10000000]">
##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [0]">
##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
##FILTER=<ID=Qual,Description="Minimum value of the QUAL field [10]">
##FILTER=<ID=VDB,Description="Minimum Variant Distance Bias (INFO/VDB) [0]">
##FILTER=<ID=GapWin,Description="Window size for filtering adjacent gaps [3]">
##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
##FILTER=<ID=SnpGap,Description="SNP within INT bp around a gap to be filtered [10]">
##FILTER=<ID=RefN,Description="Reference base is N []">
##FILTER=<ID=MinDP,Description="Minimum read depth (INFO/DP or INFO/DP4) [2]">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##FILTER=<ID=MinMQ,Description="Minimum RMS mapping quality for SNPs (INFO/MQ) [30]">
##INFO=<ID=NOVELAL,Number=.,Type=String,Description="List of samples with novel alleles">
##INFO=<ID=NOVELGT,Number=.,Type=String,Description="List of samples with novel genotypes">
##INFO=<ID=NOVELTY,Number=1,Type=Integer,Description="vcf-contrast novelty score">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C D
1 10250 . A C 61 MinMQ DP=271;VDB=0.0265;AF1=0.125;AC1=1;DP4=87,78,18,9;MQ=17;FQ=61;PV4=0.21,1,1,0.1;AN=8;AC=1;NOVELAL=D;NOVELTY=255 GT:DP:SP:GQ 0/0:60:0:99 0/0:32:5:53 0/0:50:2:83 0/1:50:3:62
1 10352 . TACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 253 MinMQ INDEL;DP=413;VDB=0.0226;AF1=0.8598;AC1=7;DP4=7,17,13,44;MQ=15;FQ=4.35;PV4=0.58,1,1,0.0055;AN=8;AC=7;NOVELAL=D;NOVELTY=6 GT:PL:DP:SP:GQ 1/1:67,6,0:18:2:11 1/1:14,7,0:12:0:12 1/1:111,22,0:23:0:26 0/1:83,0,22:28:2:18
1 17538 . C A 64 MinMQ DP=393;VDB=0.0314;AF1=0.125;AC1=1;DP4=138,205,17,27;MQ=28;FQ=64;PV4=0.87,0.32,1,1;AN=8;AC=1;NOVELAL=D;NOVELTY=29 GT:PL:DP:SP:GQ 0/0:0,152,255:148:1:99 0/0:0,29,227:72:4:34 0/0:0,71,255:86:6:76 0/1:70,0,226:81:4:65
1 28563 . A G 999 MinMQ DP=124;VDB=0.0072;AF1=1;AC1=8;DP4=22,31,27,39;MQ=18;FQ=-3.67;PV4=1,1,1,1;AN=8;AC=8;NOVELAL=D;NOVELTY=1 GT:PL:DP:SP:GQ 1/1:191,6,0:41:1:14 1/1:90,2,0:24:0:11 1/1:213,20,0:31:4:28 1/1:104,0,1:23:0:8
1 28590 . TT TTGGT 116 MinMQ INDEL;DP=112;VDB=0.0233;AF1=0.3933;AC1=3;DP4=5,46,10,16;MQ=19;FQ=54.6;PV4=0.005,1,1,0.00097;AN=8;AC=3;NOVELTY=9;NOVELGT=D GT:PL:DP:SP:GQ 0/1:80,0,2:23:10:8 0/1:9,0,9:15:15:9 0/1:51,0,26:21:2:31 0/0:0,17,39:18:5:16
1 55085 . T A 149 MinMQ DP=190;VDB=0.0199;AF1=0.3891;AC1=3;DP4=73,61,13,39;MQ=25;FQ=149;PV4=0.0003,0.35,0.01,1;AN=8;AC=3;NOVELTY=7;NOVELGT=D GT:PL:DP:SP:GQ 0/1:79,0,161:48:4:80 0/1:9,0,146:22:13:10 0/1:68,0,250:49:12:69 0/0:0,7,228:67:12:7
1 58176 . G A 94.7 MinMQ DP=93;VDB=0.0330;AF1=0.3746;AC1=3;DP4=51,13,15,9;MQ=17;FQ=94.7;PV4=0.11,0.0027,1,1;AN=8;AC=3;NOVELTY=18;NOVELGT=D GT:PL:DP:SP:GQ 0/1:30,0,23:22:0:26 0/1:18,0,15:12:7:17 0/1:55,0,102:29:2:56 0/0:0,42,114:25:9:41
1 66507 . T A 999 PASS DP=202;VDB=0.0385;AF1=0.626;AC1=5;DP4=25,14,63,82;MQ=42;FQ=999;PV4=0.03,0.023,1,0.0014;AN=8;AC=5;NOVELTY=20;NOVELGT=D GT:PL:DP:SP:GQ 0/1:255,0,205:42:7:99 0/1:255,0,20:37:12:21 0/1:255,0,155:57:4:99 1/1:255,72,0:48:0:71
1 66521 . TATATAATATA TATATAATATAATATA 999 PASS INDEL;DP=200;VDB=0.0384;AF1=0.3747;AC1=3;DP4=61,75,25,12;MQ=43;FQ=999;PV4=0.016,1,3.8e-20,0.38;AN=8;AC=3;NOVELTY=25;NOVELGT=D GT:PL:DP:SP:GQ 0/1:233,0,255:40:7:99 0/1:25,0,255:32:16:26 0/1:178,0,255:56:3:99 0/0:0,75,255:45:3:74
1 73841 . C T 999 PASS DP=182;VDB=0.0366;AF1=0.3748;AC1=3;DP4=50,64,12,26;MQ=30;FQ=999;PV4=0.25,1.6e-10,0.084,1;AN=8;AC=3;NOVELTY=28;NOVELGT=D GT:PL:DP:SP:GQ 0/1:95,0,255:33:3:96 0/1:174,0,204:27:9:99 0/1:28,0,255:53:17:29 0/0:0,64,255:39:6:63
X 2 . A G 89 PASS DP=304;VDB=0.0327;AF1=0.125;AC1=1;DP4=99,171,10,15;MQ=30;FQ=89;PV4=0.83,0.3,0.035,1;AN=8;AC=1;NOVELTY=255;NOVELGT=D GT:PL:DP 0/1:95,0,255:11 0/0:0,72,255:11 0/0:0,101,255:11 1:255,0:11
X 3 . A G 89 PASS DP=304;VDB=0.0327;AF1=0.125;AC1=1;DP4=99,171,10,15;MQ=30;FQ=89;PV4=0.83,0.3,0.035,1;AN=8;AC=1;NOVELAL=D;NOVELTY=255 GT:PL:DP 0/0:0,95,255:11 0/0:0,72,255:11 0/0:0,101,255:11 1:255,0:11
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