Table III.

Imputation accuracy rates (in percent) of filtered SNPs (with MACH Rsq over 0.3) using HapMap II (HMII) and 1000 Genomes (1KG) data across the MAF spectrum. Red boldfaced are highest accuracy rates for each masked data. Imputation accuracy rates of all imputed SNPs are shown in Supplementary Table I.

Masking Rate	Public Data	Strategy	MAF spectrum			Polymorphic SNPs			Overall Accuracy
			Rare	Low Freq	Common	CEU- specific	YRI- specific	in both panels
5%	HMII	YRI	17.8	64.0	80.9		75.6	80.1	79.3
		CEU	22.7	38.6	56.8	30.3		56.2	52.4
		INT	34.7	69.8	83.0			82.0	82.0
		UNI	46.5	66.2	83.3	54.4	76.6	83.2	78.0
		MER	22.1	52.6	80.1	30.3	75.6	80.1	73.5
	1KG	YRI	15.4	64.5	81.2		77.7	80.9	80.2
		CEU	23.0	39.0	57.9	31.7		58.2	54.3
		INT		70.1	82.5			82.0	82.0
		UNI	50.1	65.8	82.5	56.9	77.5	84.0	78.9
		MER	23.0	49.5	80.0	31.7	77.7	80.9	74.5
50%	HMII	YRI	24.9	56.9	74.5		70.5	74.1	73.5
		CEU	26.0	34.4	51.2	35.7		50.6	49.6
		INT	56.9	62.7	76.2			75.6	75.6
		UNI	49.9	61.4	76.8	59.0	70.4	77.0	75.1
		MER	26.0	47.3	73.9	35.7	70.5	74.1	71.4
	1KG	YRI		61.2	76.4		71.9	76.7	75.8
		CEU	20.1	35.4	54.1	37.7		54.1	52.5
		INT		63.7	77.4			77.1	77.1
		UNI	48.2	62.0	77.9	58.9	71.9	79.3	76.4
		MER	19.7	45.0	75.4	37.7	71.9	76.7	72.9
80%	HMII	YRI		50.0	62.5		58.7	62.6	62.0
		CEU	18.9	30.3	42.0	32.2		41.6	41.0
		INT		53.4	63.1			62.8	62.8
		UNI	49.3	53.3	63.4	55.8	57.5	63.8	62.7
		MER	17.8	40.8	62.1	32.2	58.7	62.6	60.5
	1KG	YRI		58.3	68.3		65.0	68.6	68.0
		CEU	22.6	33.4	47.2	34.7		47.3	46.3
		INT		60.8	66.6			66.5	66.5
		UNI	50.1	58.7	68.2	56.6	66.0	68.8	67.7
		MER	20.6	39.8	67.4	34.7	65.0	68.6	65.6

Rare variants with MAF ≤ 0.01; Low frequency variants with 0.01 < MAF ≤ 0.05; Common variants with MAF > 0.05

INT refers the intersection strategy; UNI refers the union strategy; MER refers the merge strategy

CEU-specific SNPs are polymorphic only in CEU; YRI-specific SNPs are polymorphic only in YRI; SNPs in both panels are polymorphic in both CEU and YRI