Table 2.

Simulation results for clustering of biallelic effects using our presentation (eq. (1)) of the infinite alleles model when markers are fully informative. 100 replicates were simulated for each QTL effect

Percentage of the phenotypic variance explained by the QTL	Proportion correctly clustered allele effects	Cluster differencea	Estimated allelic QTL varianceb ($\frac{1}{2}{\sigma }_v^2$)	Estimated dominance variance (${\sigma }_d^2$)	Estimated residual variance
5% additive QTL	0.79	2.63 (0.81)	2.65 (1.16)	-	95.11 (4.85)
10% additive QTL	0.93	3.93 (0.73)	4.99 (1.58)	-	89.85 (4.97)
20% additive QTL	0.97	5.91 (0.65)	9.89 (2.44)	-	78.98 (3.87)
20% add. and 10% dom	0.99	5.39 (1.85)	9.61 (4.46)	10.98 (3.1)	70.43 (2.56)

^a Average differences between cluster means. Standard deviations within parentheses

^b The allelic variance is estimated from model (1). The expected mean is half the proportion of the total variance explained by the QTL.