TABLE 3.

F_ST values generated for A. Coho salmon (Oncorhynchus kisutch) and B. Bull trout (Salvelinus confluentus) RADseq datasets using different reference genomes and genotypers. Provided are the 95% confidence intervals (in parentheses) for the point estimates. The reference genomes tested are abbreviated (Okis = O. kisutch, Otsh = O. tshawytscha, Omyk = O. mykiss, Salp = Salvelinus alpinus, Ssal = Salmo salar, Tthy = Thymallus thymallus). Genomes are ordered from top to bottom by increasing phylogenetic distance from the Coho salmon (Okis). De novo refers to the assembly pipelines of Stacks and dDocent, which uses FreeBayes to genotype. The Atlantic salmon genome (Ssal) processed with FreeBayes produced no useable SNPs

(A) Genome	ANGSD	FreeBayes	Stacks	De novo
Oncorhynchus kitush	0.014 (0.014–0.015)	0.031 (0.029–0.033)	0.053 (0.049–0.057)
Oncorhynchus tshawytscha	0.008 (0.007–0.008)	0.026 (0.023–0.028)	0.035 (0.032–0.039)
Oncorhynchus mykiss	0.006 (0.006–0.006)	0.026 (0.023–0.029)	0.03 (0.027–0.034)
Salvelinus alpinus	0.003 (0.002–0.003)	0.017 (0.014–0.02)	0.013 (0.011–0.015)
Salmo salar	0.004 (0.003–0.004)	NA	0.023 (0.02–0.026)
Thymallus thymallus	0.002 (0.001–0.002)	0.01 (0.01–0.01)	0.007 (0–0.016)
FreeBayes				0.01 (0.01–0.02)
Stacks				0.05 (0.05–0.06)

(B) Genome	ANGSD	FreeBayes	Stacks	De novo
Oncorhynchus kitush	0.02 (0.02–0.02)	0.27 (0.26–0.28)	0.28 (0.27–0.3)
Oncorhynchus tshawytscha	0.02 (0.02–0.02)	0.28 (0.27–0.3)	0.28 (0.27–0.29)
Oncorhynchus mykiss	0.02 (0.02–0.02)	0.26 (0.25–0.27)	0.27 (0.25–0.28)
Salvelinus alpinus	0.06 (0.05–0.06)	0.42 (0.41–0.43)	0.35 (0.34–0.35)
Salmo salar	0.03 (0.03–0.03)	NA	0.31 (0.3–0.32)
Thymallus thymallus	0.01 (0.01–0.01)	0.08 (0.07–0.09)	0.08 (0.04–0.12)
FreeBayes				0.28 (0.28–0.29)
Stacks				0.51 (0.5–0.52)