More MUMmer questions

Question

[skbrimer]

My virus needs all 10 segments to be a functional virus. From this mummer coverage map(sorry for the bad resolution) developed using promer. This map, to me, would imply that I have at least 2 populations. One that is very closely related to my reference (~>90%) and one closely related at ~80% similarity. Plus an extra copy of one gene in the 60% to ref (which I can only assume is there to troll me). The 80ish percent similar group has all the genes, while the 90% is missing one so I would pick the 80% if I had to choose one.

The question of the hour is, am I interrupting this output correctly?

Answer 1

[skbrimer]

Alright, it took a day however I think I have finally figured out what is going on here. Mummer, specifically promer, looks at the amino acid translations. All six frames. So from what I can figure from the show-coords output the coverage graph is showing me each contig's %ID to the ref in each reading frame.

So It is not a mixed population, just a newbie looking at it incorrectly.