Table 3.

Number of outliers (FDR q < 0.05) identified using BayeScan and OutFLANK on data sets containing just the coastal samples (AD06, UP03, KOD03, PWS12, HS04, and WC05) and another data set containing only the southeast samples (WC05 and HS04 vs SS12/13)

	BayeScan Coastal	BayeScan Southeast	OutFLANK Coastal	OutFLANK Southeast
BayeScanCoastal	76, 48 (54, 14)
BayeScanSoutheast	2 (1, 0)	9, 4 (6, 1)
OutFLANKCoastal	65 (44, 14)	3 (2, 0)	77 (54, 13)
OutFLANKSoutheast	1 (1, 0)	7 (5, 1)	2 (2, 0)	36 (26, 2)

Numbers on the diagonal represent the total number of outliers identified by each test for each data set—for the two BayeScan analyses, the second number is the number of loci with decisive evidence for selection (log(PO)>2). Numbers below the diagonal represent the number of outliers in common between the two analyses. Numbers within parentheses represent how many outliers aligned uniquely to the Atlantic cod genome (gadMor1) and number of outliers that aligned uniquely to a coding region, respectively.