Fig. 15

Examples of good (green boxes, score 1) and bad (red boxes, score 3) quality SNP markers. In each panel, a scatterplot of 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: a good quality SNP marker; a good quality SNP marker with a slightly low fluorescence intensity; a good quality SNP marker with a slightly high fluorescence intensity; a good quality SNP marker with moderately compressed but separated clusters; a bad quality SNP marker with a very low calling rate because of low fluorescence intensity; a bad quality SNP marker with very compressed and overlapping clusters; a bad quality SNP marker with too low fluorescence intensity; a bad quality SNP marker with random fluorescence intensity and no cluster; a bad quality SNP marker with multiple and overlapping clusters