TABLE 2.

Power for standard GEMMA, GEMMA LOCO, and subpopulation meta-analysis applied to the two simulation settings with cis effects in the 43 strain 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 by the corresponding model.

Method	Power: One cis effect	Power: Multiple cis effects
Standard GEMMA	0.67	0.63
GEMMA LOCO	0.68	0.64
Subpop Meta	0.50	0.47