I want to calculate the mutation rate for a codon using the mpileup files I generated from paired end reads.
I have 60 samples all mapped to the same reference. So how do I calculate a mutation rate for a codon using the read quality and coverage data? Is there a program that already does this, or is there an algorithm for which I can use for my own script?
I have predicted sites of positive selection, I would like to see if the sequencing reads reflect this prediction.