Table1.

Simulation study results

	Enr.	Strat.	Rejected	FDP
0.00	None	None	1 [0,5]	1.00 [0.00,1.00]
0.00	None	Low	4 [0,15]	1.00 [0.00,1.00]
0.001	None	None	79 [45,137]	0.25 [0.11,0.42]
0.001	None	Low	19 [4,70]	0.55 [0.19,0.79]
0.001	Low	None	92 [62,149]	0.30 [0.00,0.46]
0.001	Low	Low	17 [4,77]	0.44 [0.00,0.70]
0.001	High	None	90 [63,132]	0.28 [0.13,0.41]
0.001	High	Low	17 [5,47]	0.46 [0.21,0.67]
0.01	None	None	7 [1,19]	0.00 [0.00,0.17]
0.01	None	Low	6 [1,18]	0.25 [0.00,0.85]
0.01	Low	None	43 [17,101]	0.10 [0.00,0.20]
0.01	Low	Low	9 [1,38]	0.23 [0.00,0.67]
0.01	High	None	60 [16,124]	0.11 [0.00,0.23]
0.01	High	Low	8 [1,28]	0.14 [0.00,1.00]
0.05	None	None	4 [0,17]	0.00 [0.00,0.17]
0.05	None	Low	4 [0,15]	0.00 [0.00,1.00]
0.05	Low	None	39 [8,106]	0.00 [0.00,0.07]
0.05	Low	Low	8 [2,25]	0.00 [0.59,0.23]
0.05	High	None	47 [18,101]	0.00 [0.00,0.07]
0.05	High	Low	8 [1,27]	0.00 [0.00,0.23]

Note: Median number of SNPs rejected (Rejected) and FDP for the proposed cmfdr methodology. Settings include level of polygenicity (), level of covariate enrichment (Enr.) and level of population stratification (Strat.). Numbers in brackets give middle 95% of distributions across 100 simulations for each setting. A SNP was rejected if its cmfdr was . Details of simulation settings and more extended comparisons are given in the Supplementary Materials.