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##fileformat=VCFv4.1
##Goby=UNKNOWN
##FieldGroupAssociations=INFO/pchi2-BH-FDR-q-value=q-value,INFO/pchi2-BH-FDR-q-value=indexed,CHROM=genomic-coordinate,CHROM=cross-sample-field,CHROM/VALUE=genomic-coordinate,CHROM/VALUE=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,POS/VALUE=genomic-coordinate,POS/VALUE=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,ID/VALUE=external-identifiers,ID/VALUE=cross-sample-field,REF=cross-sample-field,REF/VALUE=cross-sample-field,ALT=cross-sample-field,ALT/VALUE=cross-sample-field,QUAL=cross-sample-field,QUAL/VALUE=cross-sample-field,FILTER=cross-sample-field,FILTER/VALUE=cross-sample-field,
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##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=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=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##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=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=RP,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=pchi2-BH-FDR-q-value,Number=1,Type=Float,Description="Benjamini Hochberg FDR adjusted for column pchi2-BH-FDR-q-value.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
##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">
#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=0.0001;PC2=3,3;pchi2-BH-FDR-q-value=0.002 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
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