Table 6.

Model assignment by SNP type, for each search method (using BF threshold: ln(BF) > 1) (Simulation Set 3).

2-Phenotype search				Naive search
Assigned model	True association			Assigned model	True association
	Da only	Db only	Non-causal		Da only	Db only	Non-causal
MODERATE EFFECT SCENARIO
Da and Db	0.0005	0.0023	0.0002	Da and Db	0	0	0
Da only	0.4181	0.0185	0.0267	Da only	0.4205	0.0271	0.0272
Db only	0.0196	0.4168	0.0266	Db only	0	0	0
Non-causal	0.5617	0.5624	0.9464	Non-causal	0.5795	0.9729	0.9728
STRONG EFFECT SCENARIO
Da and Db	0.0016	0.0024	0.0002	Da and Db	0	0	0
Da only	0.7077	0.0107	0.0267	Da only	0.7124	0.0285	0.0272
Db only	0.0093	0.6957	0.0266	Db only	0	0	0
Non-causal	0.2813	0.2912	0.9464	Non-causal	0.2876	0.9715	0.9728

Displays the rate at which each SNP type was assigned each model, for both the naive and 2-phenotype model searches. Recall that all SNPs that did not pass the first-pass significance threshold of ln(BF) > 1 were assigned the null model, and otherwise were assigned the most likely of the three models. The rates at which each SNP type were assigned the correct respective models are listed in bold.