TABLE 3.

Power for GEMMA LOCO applied to the two simulation settings with cis effects in the subpopulation simulations. Power is the proportion of genes with at least one nonzero cis-SNP effect that had at least one cis-SNP with a significant association identified via GEMMA LOCO analysis of the corresponding subpopulation.

Subpopulation	Power: One cis effect	Power: Multiple cis effects
FXLE/LEXF (33 strains)	0.25	0.30
HXB/BXH (30 strains)	0.53	0.52
Classic Inbred (29 strains)	0.51	0.52
HRDP (92 strains)	0.74	0.74