Genotyping design. A , The chromosome map illustrates three tiers of genotyping content present on the Toxoplasma microarray. The triangles represent the published RFLP markers, and represent genotyping capabilities prior to this work. The filled triangles represent those markers for which we have provided probesets that passed a rigorous screening process. The top half of each chromosome bar represents the EST-based SNPs, and the bottom half shows the SFPs that have passed screening. The table lists the exact numbers of SNPs represented on the array, those that passed screening, and the probe content for each. B, An expanded view of chromosome Ib indicates the SNP frequency derived from comparative sequence analysis for the three archetypal strains (see Additional File 3), and indicates the location of probesets designed for SNP detection. C, A magnified view of chromosome Ib demonstrating the overlap of SNPs with probes primarily designed for transcriptional profiling. Pink triangles indicate those probes which overlap SNP locations, and can be used to detect SFPs (see text).