Figure 2

Normalised and summarised allele intensities from the Affymetrix GeneChip array. Each SNP is represented by a pair of intensity values (A, B) for the A and B alleles, respectively (here, on a log-scale). An X chromosome SNP is shown, clearly indicating separation into distinct genotype clusters. The plot also shows that different copy numbers can be distinguished. Males are haploid for the particular SNP (ie either AY or BY) and show up as homozygous but with reduced allele intensity. Grey: BY; blue: BB; green: AB; red: AA; and pink: AY.