gene_analyses.R issue

[bighawkin]

By run the code of gene_analyses.R I get the picture. It seems something wrong.

I have some question confused me:
are mutations/length means mutation rate?
I see the detail in the code" mutations=sum((SNV+InDel)", so the artical caculate muation rate combine SNV and Indel? not de novo SNV mutation rate or de novo Indel muation rate?
Thank you.