I am new to the SNP calling analysis and my question regard "expectations". I am trying to compare 3 de novo assemblies for calanoid copepod (non-model) and I would like to use the SNP calling as a way to assess the genetic variation between individuals. I do know from other paper that high genetic diversity is expected in my species and I am trying to link the SNP calling with this. I have seen that for humans 0.1% of SNPs diversity is enough to claim that 2 individuals are from different population but I am not sure if I can use this "expected" value also for copepods.
So my question is: Is there a way, based on % of "shared" and unique SNPs that I can support my theory of genetic diversity? Any "magic number" that would support the difference between individuals?
Thanks for the help,