Table 5.

Comparison of probabilities that causal variants (cvs) have rank 10 or less, from flashfm and fastPAINTOR, varying sample size.

	Trait 1 (E+G)
	Pr(1 or more cvs rank <= 10)		Pr(Both cvs rank <= 10)
N	flashfm	fastPAINTOR	flashfm	fastPAINTOR
1000	0.797	0.493	0.243	0.083
2000	0.937	0.757	0.530	0.187
3000	0.987	0.823	0.677	0.303
4000	1.000	0.870	0.847	0.403
5000	0.997	0.887	0.867	0.457

	Trait 2 (E+H)
	Pr(1 or more cvs rank <= 10)		Pr(Both cvs rank <= 10)
N	flashfm	fastPAINTOR	flashfm	fastPAINTOR
1000	0.747	0.463	0.133	0.057
2000	0.917	0.617	0.370	0.130
3000	0.960	0.737	0.600	0.237
4000	0.987	0.783	0.717	0.297
5000	0.997	0.857	0.783	0.353

For all sample sizes, flashfm consistently has larger probabilities than those from fastPAINTOR. Flashfm has twice the probability of fastPAINTOR for both causal variants to have rank 10 or lower. Two traits were simulated to have causal variants E+G and E+H and trait correlation is 0.4. Sample size ranges from N = 1000 to 5000. The region has 1231 SNPS and was simulated to mimic the LD structure of the CTLA4 region, 2q-204446258-204816382 (GRCh37/hg19). Results are based on 300 replications.