Table 4.

Application of AVENGEME to Normally Distributed Traits Simulated on Real Genotypes

	Pruned		Clumped		Independent
r2	0.1	0.2	0.1	0.2	0.1	0.2
Mean ${\hat{\sigma }}_1^2$	0.173	0.281	0.297	0.389	0.297	0.300
SD ${\hat{\sigma }}_1^2$	0.041	0.053	0.042	0.05	0.039	0.046
Mean ${\hat{\pi }}_{01}$	0.559	0.579	0.900	0.879	0.949	0.931
SD ${\hat{\pi }}_{01}$	0.428	0.400	0.066	0.080	0.02	0.096

Terms are as follows: pruned, markers are randomly retained in the reduced set; clumped, most strongly associated markers are greedily retained in the reduced set; r², threshold on residual pairwise LD within the reduced set; independent, results for simulated markers with no LD between any pair. True ${\sigma }_1^2=0.3$, π₀₁ = 0.95.