Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

Supplementary Methods: Tasmanian devil reduced-representation sequencing. Table S1. Summary statistics for the resultant SNP loci datasets of three pipelines, filtered less stringently at a higher allowable missing data (30% call rate; cf Table 1), for Tasmanian devil (N = 131) and pink-footed goose (N = 40). Figure S1. Ratios of genotype calls between the three different pipelines for devils and geese. Figure S2. Venn diagram depicting number of shared loci between the three different pipelines for (a) devil and (b) goose. Figure S3. PCoA of the devil dataset only for the three pipelines, considering all three populations. Row one shows data processed with a call rate of 70%, row two shows data processed less stringently with a call rate of 30%. Figure S4. PCoAs of the two datasets after processing through three pipelines filtered less stringently, allowing more missing data (30% call rate). Figure S5. a) Gel image example of sample quality from 1 (highest) to 8 (no apparent DNA); b) - d) Gel quality rank (rank 7 and 8 not included as too low quality to include in study) vs. the amount of missing data of a sample for the b) Stacks, c) SAMtools and d) GATK pipelines. (ZIP 346 kb)