I have a very basic question but I don't seem to find the answer anywhere. I'm doing an SNP analysis using snippy followed by snippy core. I would like to report the amount of SNPs that were used to build the final SNP tree. While checking other papers doing these kind of things, the authors normally report 300-2000 SNPs but when I check my output (core alignment) I'm having 149.410 columns which I interpret to be SNPs, this seems a little excessive in comparison, on the other hand, to be fair, I'm analysing 342 isolates. Am I looking at the right place or should I be looking elsewhere?
Thanks a lot!