TABLE 2.

Mean of the squared differences (MSD) between observed and expected P-values for various mixed-model association- mapping methods as well as Spearman's rank correlation coefficient ρ between the P-values of one- and two-stage association-mapping approaches

	MSD
Two stage		Spearman's ρ
Method	R1 matrix	R2 matrix	One stage	R1 matrix	R2 matrix
QK	0.010	0.013	0.088	0.74	0.79
PK	0.011	0.024	0.091	0.73	0.75
K	0.016	0.022	0.061	0.67	0.69
G	0.077	0.090	0.090	0.63	0.64
Kunrel	0.013	0.016	0.042	0.63	0.76
QK0.70	0.003	0.003	0.002	0.84	0.93
PK0.70	0.002	0.005	0.003	0.87	0.93
K0.70	0.015	0.020	0.009	0.76	0.88
K0.35	0.010	0.011	0.004	0.63	0.80