Hi,
I was examining the pileup by Samtools at a particular base of interest:
X 131016403 G G 103 0 60 53 T$T,,.t.....T.TT,,,..,.t,,...,t,t,tTT,.TT..T..Tt,,T,,t BFGGAGCEFEEE<B-GGGAGGFGGGGGG?GGFGGGGGBEGFGGGEGEFDGGEF
It looks like a clear heterozygous position with good coverage and decent base qualities, however it got a SNP quality score of 0 and a homozygous genotype call. Is there any possible explanation for this?![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
The data are from 75x2 PE reads and alignment was done using ELANDv2. Any help on this will be highly appreciated. Thanks!
I was examining the pileup by Samtools at a particular base of interest:
X 131016403 G G 103 0 60 53 T$T,,.t.....T.TT,,,..,.t,,...,t,t,tTT,.TT..T..Tt,,T,,t BFGGAGCEFEEE<B-GGGAGGFGGGGGG?GGFGGGGGBEGFGGGEGEFDGGEF
It looks like a clear heterozygous position with good coverage and decent base qualities, however it got a SNP quality score of 0 and a homozygous genotype call. Is there any possible explanation for this?
![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
The data are from 75x2 PE reads and alignment was done using ELANDv2. Any help on this will be highly appreciated. Thanks!
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