Figure 3: Genotyping quality control.

(a) Genotyping samples shown in the hybridization signal space (A−B; (A+B/2)) used by BRLMM-P for calling genotypes. A and B are the raw hybridization signals in the CEL files. Each dot represents a sample. Homozygote calls are coloured in red and yellow, heterozygote calls in orange and uncalled samples in blue. Only markers showing three large, well-resolved clusters with few uncalled samples were selected for haplotype reconstruction. (b) Principal component analysis (PCA) of the genotype calls. Each dot is a sample. The position of the samples on the first two principal components. Those samples genotyped at CNG are coloured in blue, those genotyped at the MDC in red. The genotypes were encoded as 0,1,2 for this analysis, missing values were replaced by the minor allele frequency of the SNP, and the PCA was carried out without centering or scaling the genotypes.