Table 1. Type-I error rates of various imputation-based association methods for the causal SNP under the significant level of 5%.

	Quantitative Trait			Qualitative Trait
	Low-LD	Medium-LD	High-LD	Low-LD	Medium-LD	High-LD
Genotyped-1 SNP/6kb	5.0	5.2	5.1	4.9	5.1	4.3
Ideal	5.1	5.0	5.0	5.0	5.1	5.1
SNPTEST	5.0	5.0	4.8	5.0	5.0	4.8
SNPTEST-BG	5.0	5.0	5.1	5.0	5.1	5.1
MACH2qtl/dat	5.0	5.0	5.0	4.9	4.9	5.0
BIMBAM	5.0	4.8	5.0	5.0	4.8	5.0
Beagle	-	-	-	4.9	5.1	4.9
Plink	-	-	-	4.4	4.3	4.4
ProbABEL	5.1	5.1	5.0	5.1	5.2	5.1
SNPMStat	-	-	-	7.0	6.0	4.7