Table 1.

Type I error and power

	Type I errora			Powerb
Method	0.05	0.005	0.0005	Chr 6	Chr 11	Chr 18
Single-SNP association	0.051	0.0048	0.00057	1.0	0.7	0.1
Haplotype association	0.053	0.0052	0.00051	1.0	0.8	0.1
HSS	0.052	0.0046	0.00031	1.0	1.0	0.1
CROSS	0.051	0.0051	0.00061	1.0	1.0	0.4

^aType I results at three different significance levels were determined from the Replicates 1 to 10 of SNPs on all chromosomes except 6, 11, and 18.

^bPower is determined as the fraction of replicates showing a significant result (p < 0.05/9187) in a 1-Mb region around SNP6_153 on chromosome 6, SNP11_389 on chromosome 11, and SNP18_269 on chromosome 18.