Table 2:

Deviation (%) between P-, β and SE values computed by SNPTEST (ST), QuickTest (QT) and RegScan (RS) based on 40 765 random markers

Parameter	RS versus QT	RS versus ST	QT versus ST
Mean deviation of P-values (%)	0.119	0.114	0.006
P-values with >5% deviation (%)	0.000	0.010	0.010
P-values with >1% deviation (%)	2.956	2.951	0.010
Mean deviation of β (%)	0.018	0.017	0.036
β values with >5% deviation (%)	0.373	0.383	0.010
β values with >1% deviation (%)	1.820	1.828	0.010
Mean deviation of SE (%)	0.004	0.004	0.0002
SE values with >5% deviation (%)	0.000	0.007	0.007
SE values with >1% deviation (%)	0.000	0.010	0.010

The deviation (%) is calculated as the mean of the deviations of all markers (each calculated as the larger value divided by the smaller value times 100).