heterozygous genotype in bacterial snp calling

Question

[manjumoorthy95]

I did snp calling for bacterial strains using GATK HaplotypeCaller. The genotypes in the result obtained had, heterozygous variants present in it. Is this possible, since bacteria are haploid.

Answer 1

[swbarnes2]

It's either an error in mapping due to a bigger discrepancy than a SNP, or it's a repetitive region with slight differences between the loci, or your sample is not clonal. I'd start by eyeballing the regions in IGV, and blast the flanking sequence to see if it's known to be repetitive.

[manjumoorthy95]

Ok thank you. Let me try out that way