Does bcftools distinguish between two gene copies on the bacterial genome ?

Question

[praneeth.bommisetti]

Hey everyone,

So I have used bcftools "mpileup" in combination with the multi-allelic caller to discover mutations in desired bacterial RNA samples. Here is some data given out by the bcftools.

Now comparing the sequences of these genes:

So basically, two each of the genes in the first image have the same sequences. I am wondering, how bcftools is able to differentiate between the two genes that share same transcripts. I am asking such a question because it is giving me two different qual values for two genes with the same sequence.

Can anyone shed some light?

Thank you