mutations versus homologous recombination (r/m)

[Thexiyang]

Hi. One question on the r/m. I did not find r/m values in the inStrain output. In the paper, it said: "The relative rate of recombination to mutation (gamma/mu) for each population was calculated using the mcorr package (cite) on synonymous third position codon sites across filtered mapped reads from all samples. " This is not clear to me. Could you provide some further guidance to calculate this parameter based on output from inStrain? Thanks!

[alexcritschristoph]

Hello, that metric was calculated in the paper using mcorr: https://www.nature.com/articles/s41592-018-0293-7 https://github.com/kussell-lab/mcorr