VCF file - If format is GT:PL what does 1:161, 0 mean for GT column

Apologies if this is a stupid question I have a vcf file with multiple samples with different ranges for the GT (genotype) value.

CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Sample1 Sample2 Sample3 Sample4 Sample5
NC_011993.1_Escherichia_coli_LF82_complete_genome_length_4773108    268226  NC_011993.1_Escherichia_coli_LF82_complete_genome_length_4773108_268226_CA_C    CA  C   228 PASS    INDEL;IDV=13;IMF=1;VDB=0.7156;SGB=-0.680642;MQSB=0.898397;MQ0F=0;MQ=34;DP=3055;DP4=50,228,1419,1358;AN=75;AC=75 GT:PL   1:161,0 1:252,0 1:255,0 1:158,3 1:200,0

1 indicates the presence of the alternate allele, (C in the example) but what does the value/range after the colon mean?

bcftools vcf

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written 5.1 years ago by Linda •

column FORMAT isGT:PL . So you should find a description in the header abour GT and PL

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

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written 5.1 years ago by Pierre Lindenbaum

Sorry I worded that badly - what does the 161 mean in 1:161?

I'm understanding that 1:161 has something to do with the genotype while

0 is the phred score?

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written 5.1 years ago by Linda •

0 answers

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