TABLE 3.

Detection and estimation for simulated QTL in case II

				Effectd				Inferred modee
Simulated QTL	Methoda	Powerb	Positionc	2a	apat	amat	d	E1	E2	E3	E4
QTL1 (LG1: 25 cM, E4) (amat = −0.25)	Bayes	0.80	25.3 (4.1)	—	—	−0.26 (0.04)	—	0.01 (0.04)	0.01 (0.11)	0.00 (0.00)	0.78 (0.85)
	IM	0.57	28.4 (12.6)	—	—	−0.21 (0.02)	—	0.01	0.21	0.15	0.20
QTL2 (LG1: 75 cM, E1) (2a = 0.5, d = 0.0)	Bayes	0.99	75.4 (3.6)	0.47 (0.08)	—	—	0.03 (0.11)	0.95 (0.83)	0.02 (0.14)	0.02 (0.02)	0.00 (0.01)
	IM	0.98	76.1 (3.9)	0.39 (0.07)	—	—	0.02 (0.14)	0.67	0.14	0.17	0.00
QTL3 (LG2: 65 cM, E3) (apat = 0.2)	Bayes	0.71	61.9 (9.7)	—	0.21 (0.04)	—	—	0.07 (0.13)	0.03 (0.14)	0.61 (0.72)	0.00 (0.01)
	IM	0.64	62.6 (12.5)	—	0.24 (0.03)	—	—	0.12	0.04	0.48	0.00

The proportions of MCMC iterations fitting QTL1 and QTL2 simultaneously in each analysis were averaged as 0.82 ± 0.27.

^aBayes, Bayesian method; IM, interval mapping.

^bProportion of replicates that successfully detected each QTL with genomewide significance level of P = 0.05 in a total of 100 replicates.

^cAverage of estimated QTL positions calculated in the replicates with successful detection of QTL with standard deviations given in parentheses.

^dAverage of estimated QTL effects corresponding to the simulated expression mode over the replicates with successful QTL detection with standard deviations given in parentheses.

^eProportion of replicates supporting each QTL expression mode as the most probable state in the replicates with successful detection of QTL. Averages of posterior probabilities of QTL expression modes are given in parentheses for the Bayesian method. Prior probabilities of expression modes E₁, E₂, E₃, and E₄ were 0.6, 0.2, 0.1, and 0.1, respectively, and transition probabilities among expression modes were set at δ = 0.2, κ = 0.6, ω = 0.1, η = 0.1, and ζ = 0.1.