Table 2.

Imputation Accuracy into All Available Individuals of European Ancestry

	Imputation with MTFS sequences			Imputation with 1000 Genomes Aug 2011 release
	N	Mean RSQ	RSQ > .3	N	Mean RSQ	RSQ > .3
< .001	11,874,879	.479	78.8%	19,028,251	.278	35.5%
MAF [.001–.005)	5,137,513	.639	95.8%	6,641,963	.456	64.9%
MAF [.005–.01)	1,325,092	.764	98.5%	1,690,255	.568	79.7%
MAF [.01–.05)	2,673,865	.862	99.0%	3,022,145	.726	90.1%
MAF ≥ .05	5,872,931	.965	99.5%	6,604,512	.911	97.3%

Note. SNPs were selected using the 1000 Genomes imputed minor allele frequency. RSQ = minimac-estimated quality metric based on the imputation hidden Markov model; RSQ > .3 = percentage of variants with minimac RSQ greater than .3, a conventional threshold used to discard poorly imputed variants.