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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
##reference=file://xxx//mpileup.ref.fa.gz
##contig=<ID=X,length=81195210>
##ALT=<ID=X,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group 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=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=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##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=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102
X 302 . T TA 999 . INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;AF1=0.685575;AC1=4;DP4=2,4,8,11;MQ=51;FQ=61.4911;PV4=1,1,1,1 GT:PL:DP:DV 0/1:167,0,96:11:6 0:157,0,9:7:6 1/1:201,21,0:7:7
X 828 . T C 999 . DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;AF1=0.656389;AC1=4;DP4=2,4,8,11;MQ=60;FQ=89.3748;PV4=1,1,1,0.32233 GT:PL:DP:DV 0/1:211,0,35:12:10 0:116,91:9:5 1/1:120,12,0:4:4
X 834 . G A 999 . DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;AF1=0.646503;AC1=4;DP4=2,3,7,10;MQ=60;FQ=68.6952;PV4=1,1,1,0.228905 GT:PL:DP:DV 0/1:185,0,46:11:9 0:128,59:8:5 1/1:89,9,0:3:3
X 1665 . T C 3.14059 . DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;AF1=0.167199;AC1=1;DP4=7,11,1,1;MQ=56;FQ=3.56819;PV4=1,0.239991,0.0798553,0.27333 GT:PL:DP:DV 0/0:0,21,185:7:0 0:0,222:9:0 0/1:35,0,51:4:2
X 1869 . A T 134.348 . DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;AF1=0.598209;AC1=4;DP4=6,9,5,4;MQ=59;FQ=138.299;PV4=0.675175,0.0234896,1,0.324361 GT:PL:DP:DV 0/1:115,0,224:18:7 0:16,104:5:1 1/1:42,3,0:1:1
X 2041 . G A 999 . DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;AF1=0.665982;AC1=4;DP4=6,5,12,7;MQ=59;FQ=999;PV4=0.71163,1,0.228209,0.143795 GT:PL:DP:DV 0/1:229,0,212:21:11 0:32,24:2:1 1/1:223,21,0:7:7
X 2220 . G A 999 . DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AF1=0.656341;AC1=4;DP4=6,2,1,11;MQ=59;FQ=139.373;PV4=0.00443756,1,1,1 GT:PL:DP:DV 0/1:139,0,130:12:6 0:69,46:4:2 1/1:131,12,0:4:4
X 2564 . A G 227.769 . DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;AF1=0.656337;AC1=4;DP4=1,4,4,5;MQ=60;FQ=97.3723;PV4=0.58042,1,1,1 GT:PL:DP:DV 0/1:88,0,78:6:3 0:57,56:4:2 1/1:124,12,0:4:4
X 3104 . C T 24.364 . DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;AF1=0.170892;AC1=1;DP4=8,15,2,0;MQ=59;FQ=25.179;PV4=0.15,1,1,1 GT:PL:DP:DV 0/0:0,48,255:16:0 0:0,144:4:0 0/1:59,0,93:5:2
X 3587 . G A 353.302 . DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;AF1=0.665739;AC1=4;DP4=4,7,10,6;MQ=60;FQ=358.057;PV4=0.25186,0.0986321,1,1 GT:PL:DP:DV 0/1:161,0,184:14:7 0:22,118:5:1 1/1:212,24,0:8:8
X 3936 . A G 999 . DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;AF1=0.666004;AC1=4;DP4=5,6,6,17;MQ=57;FQ=999;PV4=0.434446,0.125787,1,1 GT:PL:DP:DV 0/1:233,0,206:20:11 0:77,58:6:4 1/1:196,24,0:8:8
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