Fig. 3.

Comparison of genotype calls and continuous genotypes. Comparison of continuous values and genotype calls for three selected probes. a-c, d-f and g-i are the disease, flowering and growth trait, respectively. a, d and g were generated by SuperMASSA, based on the signal intensity values of the two alleles. The shapes and colors represent genotype clusters. The expected cluster centers are indicated by solid lines. b, e and h show the correlation of the raw genotype values with the corresponding EBVs. The solid lines represent the LR. c, f and i show the correlation of the genotype classes with the EBVs. The solid lines represent the LR