. 2015 Apr 30;11(4):e1005131. doi: 10.1371/journal.pgen.1005131

Table 1. The accuracy and minor allele concordance rate of imputed genotypes.

Population	n	% of 86k SNPs that are polymorphic	% SNPs with any missing data	Imputation method (recomb. rate source)	Refer. haplo.	Mean r ² by SNP	Mean minor allele concord. (%)
Thailand(THL)	91	42%	34%	IMPUTE2	90 THL	0.51	31.8
				(GB4x7G8)	471 ALL	0.70	66.5
				IMPUTE2	90 THL	0.53	38.2
				(HB3xDD2)	471 ALL	0.70	67.2
				IMPUTE2	90 THL	0.56	46.1
				(LDhat)	471 ALL	0.71	70.7
				BEAGLE	90 THL	0.92	91.4
				(map free)	471 ALL	0.27	29.0
Cambodia (CBO)	253	60%	45%	IMPUTE2	252 CBO	0.77	68.8
				(GB4x7G8)	471 ALL	0.87	82.5
				IMPUTE2	252 CBO	0.78	73.7
				(HB3xDD2)	471 ALL	0.88	83.2
				IMPUTE2	252 CBO	0.84	79.1
				(LDhat)	471 ALL	0.90	86.1
				BEAGLE	252 CBO	0.96	92.1
				(map free)	471 ALL	0.65	63.3
Gambia (GMB)	55	38%	38%	IMPUTE2	54 GMB	0.99	95.4
				(GB4x7G8)	471 ALL	0.99	95.2
				IMPUTE2	54 GMB	0.99	95.4
				(HB3xDD2)	471 ALL	0.99	95.4
				IMPUTE2	54 GMB	0.99	95.4
				(LDhat)	471 ALL	0.99	95.4
				BEAGLE	54 GMB	0.90	87.1
				(map free)	471 ALL	0.21	23.0
Malawi (MLW)	60	41%	37%	IMPUTE2	59 MLW	0.34	9.5
				(GB4x7G8)	471 ALL	0.25	20.2
				IMPUTE2	59 MLW	0.30	9.2
				(HB3xDD2)	471 ALL	0.25	20.8
				IMPUTE2	59 MLW	0.69	49.0
				(LDhat)	471 ALL	0.26	12.3
				BEAGLE	59 MLW	0.87	85.0
				(map free)	471 ALL	0.06	6.7

Accuracy is consistently high with Beagle when only population-specific haplotypes are used as references; improves with IMPUTE when a cosmopolitan reference panel is used; and is highest with IMPUTE when LDhat-inferred recombination rates are used. ALL refers to a cosmopolitan panel including populations from the listed countries (n = 459) and Vietnam (n = 12).