Fig. 16

Examples of SNP markers included (first line with green boxes, score 13) or excluded (second line with red boxes, score 31) after visual inspection. In each panel, a scatterplot of the genotype of individuals for a SNP marker in normalized polar coordinates is represented. The x-axis is the normalized Theta (i.e., the normalized fraction of bases that are genotyped as the variant allele) and the y-axis is the normalized intensity of fluorescence of the probe. AA genotype, AB genotype, and BB genotype are depicted in red, purple, and blue, respectively. Panels from left to right and top to bottom: one SNP marker included despite cluster compression as clusters remain clearly distinct from each other; a SNP marker included despite a shift of the heterozygote cluster to the right but still distinct from the BB cluster; a SNP marker included despite a very low frequency of one of the allele but with clusters at expected position; a SNP marker excluded because of a low fluorescence intensity; a SNP marker excluded because of more than three distinct clusters; a SNP marker excluded because of ambiguity of the calling of some individuals and low fluorescence intensity