I'm completely new as-of-this-morning to ddRADseq, but am trying to get my head around the theory. If I have a 30 Mb genome and use ddRADseq with ~6500 digestion sites, how many segregating SNPs can I find (roughly)? WGS shows that there's roughly 20000 SNPs separating each isolate.
Does this depend on the amount of the reference genome covered by the ddRAD?
Any help is greatly appreciated - thanks.