Table 2.

Empirical and simulation results for all traits and commonly used thresholds

		Empirical			Simulation
		Positives		eFDRb	Positives		eFDR (SE)
		False	Truea		False	True
HDL (ntest = 19,840 ntruth = 188,577)	P = 5 × 10−8	1	16	5.9%	0.28	9.5	2.9% (0.33%)
	P = 5 × 10−7	1	18	5.3%	0.89	12	6.7% (0.45%)
	BH = 5%	1	18	5.3%	0.70	12	5.6% (0.43%)
	BY = 5%	0	14	0%	0.17	8.2	2.0% (0.31%)
	BFDP = 5%	1	17	5.6%	0.41	10	4.0% (0.37%)
LDL (ntest = 19,840 ntruth = 188,577)	5 × 10−8	0	14	0%	0.19	13	1.5% (0.19%)
	5 × 10−7	3	16	16%	0.71	16	4.2% (0.27%)
	BH = 5%	3	16	16%	0.67	16	4.0% (0.27%)
	BY = 5%	0	14	0%	0.13	12	1.1% (0.17%)
	BFDP = 5%	2	17	11%	0.37	14	2.5% (0.22%)
TG (ntest = 19,840 ntruth = 188,577)	5 × 10−8	1	8	11%	0.11	9.0	1.2% (0.21%)
	5 × 10−7	2	10	17%	0.54	10	4.9% (0.37%)
	BH = 5%	2	9	18%	0.32	10	3.1% (0.30%)
	BY = 5%	0	8	0%	0.05	8.5	0.58% (0.16%)
	BFDP = 5%	1	10	9.1%	0.36	9.8	3.6% (0.32%)
Height (ntest = 133,653 ntruth = 693,529)	5 × 10−8	0	157	0%	1.6	181	0.89% (0.042%)
	5 × 10−7	1	217	0.46%	4.9	223	2.2% (0.055%)
	BH = 5%	2	351	0.57%	22	301	6.8% (0.086%)
	BY = 5%	0	197	0%	4.3	217	2.0% (0.054%)
	BFDP = 5%	2	338	0.59%	28	317	8.1% (0.077%)
BMI (ntest = 123,865 ntruth = 681,275)	5 × 10−8	0	22	0%	0.62	39	1.6% (0.13%)
	5 × 10−7	0	37	0%	2.7	58	4.4% (0.19%)
	BH = 5%	1	41	2.4%	6.6	77	7.9% (0.19%)
	BY = 5%	0	20	0%	0.83	41	2.0% (0.15%)
	BFDP = 5%	0	35	0%	3.9	67	5.4% (0.18%)

^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.