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##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##reference=file:///seq/references/1000Genomes-NCBI37.fasta
##contig=<ID=11,length=135006516>
##contig=<ID=20,length=63025520>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##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=Dels,Number=1,Type=Float,Description="Fraction of reads containing spanning deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest contiguous homopolymer run of variant allele in either direction">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Hardy-Weinberg equilibrium test (PMID:15789306)">
##INFO=<ID=ICF,Number=1,Type=Float,Description="Inbreeding coefficient F">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total mapping quality zero reads">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth">
##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">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
X 2942109 rs5939407 T C 999 PASS DP4=23273,27816,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 1/1:255,157,0:52:99
X 3048719 . T C 999 PASS DP4=13263,27466,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 0|1:255,0,157:52:99
|
