Why num_sites not equal to num_mutations?

[silvewheat]

Hello,

I noticed that in my dataset, the num_sites is not equal to num_mutations. Is this as expected? Why they can be different?

Best,
Yudong

[benjeffery]

Hi @silvewheat!
Thanks for your question. Mutations are placed on edges in the tskit data model (https://tskit.dev/tskit/docs/stable/data-model.html) so there can be an unlimited amount of mutations at a site, changing the genotypic state for the subset of nodes underneath the mutation.