Mutation Rate Table output

[LisaCarraro]

Hallo,
if i find 36/3348654 (value obtained comparing 2 isolates) in Mutation Rate Table,
3348654 is the total number of nucleotides aligned in these 2 isolates?

Thank you very much
Best
Lisa

[fasnicar]

Hi Lisa,
The values reflect the different positions over the total number of positions that can be compared. This means that gaps, for instance, won't be considered in the mutation rates estimation. The mutation rates table is computed before any trimming and/or subsampling, if any, so will be computed on the very first multiple-sequence alignments.

I hope this helps.

Thanks,
Francesco

[LisaCarraro]

Thank you very much!!
Lisa