Table 3.

Simulations based on coalescence by ms: a comparison of type I errors and power for various methods in 500 simulations. Standard errors are given in parentheses. The high and low LD represent recombination rate per site per generation of 10⁻⁹ and 10⁻⁷, respectively. The sample consists of 1000 cases and 1000 controls

LD[#SNP†,# Hap‡]	Method	Type I error	Power
			OR = 1.5	OR = 1.75	OR = 2
High[15,16]	Single-locus scan	0.052 (0.010)	0.254 (0.019)	0.416 (0.022)	0.592 (0.022)
Phase known	Full haplotype	0.050 (0.010)	0.242 (0.019)	0.456 (0.022)	0.648 (0.021)
	CLADHC	0.042 (0.009)	0.246 (0.019)	0.464 (0.022)	0.678 (0.021)
	SHARE	0.050 (0.010)	0.312 (0.021)	0.548 (0.022)	0.728 (0.020)
Phase unknown	Haplotype score	0.034 (0.008)	0.216 (0.018)	0.462 (0.022)	0.664 (0.021)
	SHARE	0.050 (0.010)	0.308 (0.021)	0.528 (0.022)	0.738 (0.020)
Low[15,30]	Single-locus scan	0.038 (0.009)	0.154 (0.016)	0.316 (0.021)	0.420 (0.022)
Phase known	Full haplotype	0.040 (0.009)	0.116 (0.014)	0.232 (0.019)	0.370 (0.022)
	CLADHC	0.044 (0.009)	0.146 (0.016)	0.328 (0.021)	0.510 (0.022)
	SHARE	0.042 (0.009)	0.174 (0.017)	0.382 (0.022)	0.516 (0.022)
Phase known	Haplotype score	0.032 (0.009)	0.084 (0.012)	0.148 (0.016)	0.322 (0.021)
	SHARE	0.048 (0.010)	0.160 (0.016)	0.354 (0.021)	0.498 (0.022)

^†The median number of tagSNPs in 500 simulated data.

^‡The median number of common haplotypes in 500 simulations. The common haplotypes are defined as those with frequencies larger than 1%.