I’m trying to understand what exactly divergence is measuring. I’ve looked through the documentation and I see that for the nextstrain pipeline it defaults to mutations rather than mutations-per-site, and I’ve left it as default in my builds.
Is divergence measuring just the number of mutations in the sample relative to the Wuhan reference based on the alignment? If so, is this measured in nucleotide or amino acid mutations?
Additionally, I’ve noticed that the same sequence can be assigned a different level of divergence in each run, although the mutations identified don’t change. My guess is that this might be due to slight differences in the alignment, but it’s a very basic guess so please do correct me if it’s wrong.
Sorry for all the questions, and thanks in advance for any clarification!