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##fileformat=VCFv4.1
##samtoolsVersion=0.1.14 (r933:170)
##INFO=<ID=DP,Number=1,Group=DEPTHS,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,Group=RMS,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 site allele frequency of the first ALT allele">
##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
##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=RP,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##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=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT results/IPBKRNW/IPBKRNW-replicate.bam results/IPBKRNW/IPBKRNW-sorted.bam
0 145497099 . A G 17.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-30.8;QCHI2=1;PCHI2=0.752;PC2=3,3 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
1 29389393 . AC A 31.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3 GT:PL:GQ 1/1:36,3,0:42 1/1:36,3,0:42
1 44379612 . CT C 31.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3 GT:PL:GQ 1/1:36,3,0:42 1/1:36,3,0:42
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