Table 6.

Empirical and simulation results for Benjamini–Hochberg procedure

Trait	Threshold (FDR)	Empirical			Simulation
		Positives		eFDRb	Positives		eFDR
		False	Truea		False	True
HDL (ntest = 19,840 ntruth = 188,577)	5%	1	18	5.3%	0.70	12	5.6%
	10%	5	18	22%	1.3	13	8.5%
	15%	6	20	23%	1.7	14	11%
LDL (ntest = 19,840 ntruth = 188,577)	5%	3	16	16%	0.67	16	4.0%
	10%	4	16	20%	1.1	18	6.0%
	15%	7	17	29%	1.7	18	8.6%
TG (ntest = 19,840 ntruth = 188,577)	5%	2	9	18%	0.32	10	3.1%
	10%	5	10	33%	0.63	11	5.6%
	15%	5	10	33%	0.96	11	8.0%
Height (ntest = 133,653 ntruth = 693,529)	5%	2	351	0.57%	22	301	6.8%
	10%	4	421	0.94%	37	331	10%
	15%	8	468	1.7%	50	351	13%
BMI (ntest = 123,865 ntruth = 681,275)	5%	1	41	2.4%	6.6	77	7.9%
	10%	1	47	2.1%	11	91	11%
	15%	1	55	1.8%	16	102	14%

^aNumber of loci in truth set for HDL: 89, LDL: 72, TG: 60, height: 1100, BMI: 724.

^beFDR is calculated as number of false positives divided by sum of true and false positives.