Summary data from each sequencing library, A and B, with increasing sequencing depth (-m) thresholds in the ustacks module of STACKS.

The m parameter influences the number of loci generated per individual in the ustacks module of STACKS, which influences the total number of loci in the catalog and the matched loci in the sstacks module. The populations module was then run on each library independently using no population differentiation in the population map (NoPops), one population required to contain the locus (-p) and 30% of the individuals required to contain the locus (-r). Library A was generated using a 9mer probe, while library B was generated using a 10mer probe.