Table 2. .

Allelic-Imputation Error Rates

	Error Rate(%)
	Low-Density Simulateda			High-Density Simulateda			Affymetrix 500K WTCCCb
Method	Small	Medium	Large	Small	Medium	Large	Small	Medium	Large
Beaglec:
R=25	3.45	1.91	1.57	1.17	.53	.13	1.21	.87	.77
R=4	3.65	2.01	1.57	1.36	.59	.13	1.32	.88	.78
R=1	4.10	2.21	1.80	1.82	.70	.16	1.44	.94	.84
fastPHASEd:
K=20	3.37	2.54	2.80	1.19	.90	.57	1.12	.95	.93
K=10	3.91	3.19	3.43	1.72	1.38	1.04	1.21	1.05	1.04
HAP	5.26	3.66	3.89	3.20	2.55	2.31	1.68	1.38	1.33
2SNP	8.52	5.76	5.14	3.61	2.33	1.26	2.50	1.84	1.71

^aParameters for selection of tag SNPs for 1 Mb of simulated data were chosen to obtain approximate densities of 1 SNP per 10 kb (low density) or 1 SNP per 3 kb (high density). For each density, three sample sizes were considered: 100 (small), 1,000 (medium), and 5,000 (large) individuals.

^bFor the WTCCC data, sets of 200 consecutive markers were used. Three sample sizes were considered: 100 (small), 1,000 (medium), and 3,002 (large) individuals.

^cBeagle results are given for R=1, R=4, and R=25 samples per individual.

^dfastPHASE results are given for K=10 and K=20 clusters per individual.