I'm confused about how to interpret this output from calling variants using bcftools:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GSM5292852 1065632 chr9 41242177 . T C 6.65947 . DP=37;VDB=0.133454;SGB=-0.662043;RPBZ=2.91136;MQBZ=4.0715;BQBZ=1.05041;SCBZ=-0.480069;MQ0F=0;AC=2;AN=2;DP4=0,26,0,9;MQ=5 GT:PL:AD 1/1:34,24,0:26,9
In particular, I'm confused by the genotype being reported as 1/1 while the number of reads mapping to the reference vs. the alternative allele are 26 and 9, respectively.
Wouldn't this indicate a heterozygous or possibly homozygous ref. genotype?
Any insight would be much appreciated.
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made.
Thanks for your answer!