Hello,

I am current working on a comparative genomics, comparing bacterial genomes between specific species strains. After performing variant calling with Snippy and annotation with SnpEff, I noticed that most of the genomes consistently show Ts/Tv ratio around 4

I understand that a ratio around 2 is typically expected for whole-genome data. I am concerned that 4 might be too high and could indicate some issues with my analysis.

Could this be a sign of over-filtering, or is it possible to see such a high ratio due to strong purifying selection in specific bacterial species? I would appreciate any insights on whether I should re-evaluate my filtering criteria or if this could be biologically plausible.

Thanks!