TABLE 2.

The mean square error of the position estimate (MSE), the fraction of replicates with a QTL significant effect (power), the fraction of the significant QTL, where the true QTL position is within the 2-LOD-dropoff support interval [P(QTL in interval)], and correlation between estimated IBD probabilities and the IBD probability given the tree (Corr)

Analysis	MSE (cM2)	Powera	P(QTL in interval)	Size of interval (cM)	Corr
IBDHET	0.072	0.94	0.97	0.82	0.576
IBDMUT	0.049	0.95	0.97	0.58	0.537
IBDHETne	0.071	0.94	0.97	0.78	0.576
MARK1	0.088	0.83	0.11	0.11	0.357
MARK2	0.074	0.88	0.26	0.14	0.478

The IBD probability given the tree is used as the “gold standard” (see main text).

^aA nominal P-value of 0.001 was used.