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

Table 3 Population pairwise F_ST values for each analysis with 95% confidence intervals generated over 2000 bootstraps. In devils, Pop1 refers to the Western population (N = 47), Pop2 refers to the Eastern population (N = 18), and Pop3 refers to the insurance population (N = 66). In geese, Pop1 refers to the Iceland population (N = 20) and Pop2 refers to the Denmark population (N = 20)

Dataset	Pipeline	Pop 1:Pop 2	Pop 1:Pop 3	Pop 2:Pop 3
Devil (70% call rate)	Stacks	0.100 (0.090, 0.110)	0.030 (0.027, 0.034)	0.025 (0.021, 0.029)
	SAMtools	0.071 (0.056, 0.088)	0.019 (0.014, 0.025)	0.025 (0.017, 0.033)
	GATK	0.094 (0.084, 0.103)	0.029 (0.026, 0.033)	0.025 (0.021, 0.029)
Devil (30% call rate)	Stacks	0.091 (0.084, 0.100)	0.026 (0.023, 0.029)	0.025 (0.021, 0.029)
	SAMtools	0.067 (0.057, 0.078)	0.026 (0.022, 0.030)	0.015 (0.011, 0.021)
	GATK	0.091 (0.083, 0.099)	0.028 (0.025, 0.031)	0.026 (0.022, 0.030)
Goose (70% call rate)	Stacks	0.034 (0.032, 0.035)
	SAMtools	0.038 (0.036, 0.039)
	GATK	0.033 (0.032, 0.033)
Goose (30% call rate)	Stacks	0.017 (0.016, 0.019)
	SAMtools	0.092 (0.091, 0.093)
	GATK	0.046 (0.045, 0.047)

ISSN: 1471-2164