I'm analyzing a ddRAD dataset using only read 1 and I’m experiencing some interesting output in my *.u.snps.phy files. In particular, the output is producing numerous loci that aren't actually variable across my dataset. Instead, they contain a single nucleotide and N, only. For this particular file, only 1,710 loci out of the original 4,304 in the file are truly variable (def: 1 or more individual actually has a different nucleotide or is heterozygous at the locus). FYI, I've stipulated 12X coverage with 40% of individuals sharing the locus. An image of the alignment with some representative loci is attached. I’m curious if you know what’s happening here? Am I missing something?