What is the customary mutation threshold for considering a site to be mutated in a virus?
I'm working on a project where apparently viruses have different mutations depending on the ethnic background of the host. When I mapped the virus sequences to the virus genome, I noticed that there were indeed several mutations at >= 20% (that is, >= 20% of the reads have a different nucleotide at a particular genome position than the reference nucleotide). I was wondering what is the customary threshold used? This is a new field for me and I'm trying to read the literature to figure this out, but I know how awesome you biostars are, and so here I am!