Table 3.

P-values of paired t-tests comparing prediction accuracies using individual SNPs and haplotypes defined by different methods and sizes.

	Average number of SNPs per haplotype
CWT	5	10	20	50
SNP count-based haplotypes	0.002**	0.01*	0.21	0.98
Length-based haplotypes	0.0008**	0.03*	0.23	0.92
LD clustering-based haplotypes	0.0005**	0.005**	0.09	0.98
EMA	5	10	20	50
SNP count-based haplotypes	0.00004**	0.004**	0.12	0.81
Length-based haplotypes	0.00007**	0.007**	0.09	0.58
LD clustering-based haplotypes	0.0002**	0.002**	0.07	0.86
BFT	5	10	20	50
SNP count-based haplotypes	0.64	0.67	0.77	0.99
Length-based haplotypes	0.07	0.20	0.74	0.99
LD clustering-based haplotypes	0.77	0.52	0.43	1.00

* and ** indicates significant at α = 0.05, 0.01 respectively.