. 2009 Feb 27;10:94. doi: 10.1186/1471-2164-10-94

Table 3.

Mean of squared differences (MSD) between observed and expected P values for various association mapping methods in five plant species.

Method	Rapeseed

	TKW	OC	OY
ANOVA	0.0624	0.0326	0.0523
K	0.0098	0.0053	0.0016
Q₁K	0.0021	0.0047	0.0061
Q₂K	0.0013	0.0010	0.0192
PK	0.0008	0.0007	0.0026
	Potato

	GPR	PIR	PM
ANOVA	0.1928	0.0947	0.1534
K	0.0499	0.0162	0.0604
Q₁K	0.0122	0.0179	0.0389
Q₂K	0.0181	0.0017	0.0063
PK	0.0189	0.0183	0.0422
	Sugar beet

	AN	BY	CSY
ANOVA	0.1526	0.1625	0.1533
K	0.0136	0.0191	0.0173
Q₁K	0.0060	0.0239	0.0051
Q₂K	0.0118	0.0167	0.0081
PK	0.0090	0.0137	0.0065
	Maize

	EH	ED	DPS
ANOVA	0.0333	0.0147	0.0909
K	0.0003	0.0002	0.0006
Q₁K	0.0002	0.0003	0.0002
Q₂K	0.0002	0.0002	0.0003
PK	0.0003	0.0005	0.0002
	Arabidopsis

	FLC	FRI	LDV
ANOVA	0.0040	0.0004	0.0070
K	0.0006	0.0022	0.0013
Q₁K	0.0026	0.0033	0.0017
Q₂K	0.0019	0.0022	0.0013
PK	0.0021	0.0034	0.0018

For abbreviations of the analyzed traits see Table 2. For a detailed definition of the statistical models and description of the different methods see Materials and Methods.