Fig. 4.

PVE by associated markers. GAPIT 3 provides estimates of the percentage of PVE by associated markers. The proportion is a function of both magnitude of marker effects and MAF. Larger marker effects and larger MAF contribute to larger proportion of phenotypic variance explained. This relationship is demonstrated on a trait simulated from the mouse genotypes of 12,564 SNPs on 1440 individuals (available at http://gscan.well.ox.ac.uk). The simulated trait had 75% heritability with 20 QTNs. A. Markers with large magnitude that explain little phenotypic variances due to low MAF. B. Markers with large MAF that explain little phenotypic variances due to small effect. C. Markers away from the center where both MAF and marker effect are zeros that explain more variation. PVE, phenotypic variance explained.