The quality-filtered reads were then used as input data for SNP detection with Stacks v. 1.1519. First, using the ‘ustacks’ option, a set of identical reads was bundled together in a ‘stack’ and several of these stacks were merged to form putative loci with the settings: maximum dista...
1.1519. Briefly, the output data from each sample were grouped into putative loci (stacks), polymorphic sites were identified, and the putative loci were grouped together across samples. The genotypes at each puta- tive locus in each individual were then determined based on several criteria (see...