Is there any index could evaluate the polymorphic genes with SNPs and Indels in population ？

Question

[Damon_Wan]

Hello everyone, here are my questions:

I want to evaluate the polymorphic level of several genes in a population including 19 isolates. These genes containing SNPs and Indels in the mean time.

Now my solution is to filled the gaps with N of the MSA, then I calculate the average value of each identity matrix. Was it correct?

Or is there any other index can evaluate the polymorphic level, such as nucleotide diversity (Pi) is for SNPs, considering the SNPs and Indels in the mean time.

Thank you very much !