Supplementary table 5 from ddRAD sequencing resolves fine-scale population structure in a benthic invertebrate with implications for understanding phenotypic plasticity

Summary of the results obtained from different de novo assemblies of the ddRAD data generated using different values for three main parameters -m, -M and -n within the denovo_map.pl Script in Stacks. -m and -M define the minimum number of raw reads and the maximum number of mismatches between loci when creating a stack within the same individual respectively. -n corresponds to the number of mismatches allowed between loci when processing multiple individuals. For each tested combination of parameters, we report the total number of tags, the number of tags present in all of the individuals, observed heterozygosity, average depth of coverage, and the number of SNPs obtained after filtering.