The increased resolution provided by Phase II of the project is illustrated in Fig. 2. Broadly, an additional SNP added to a region shows one of three patterns. First, it may be very similar in distribution to SNPs present in Phase I. Second, it may provide detailed resolution of haplotype structure (for example, a group of chromosomes with identical local haplotypes in Phase I can be shown in Phase II to carry multiple related haplotypes). Third, the novel SNP (or group of added SNPs) may reveal previously missed recombinant haplotypes. The extent to which each type of event occurs varies among populations and chromosomal regions. The greatest gains in resolution, in terms of identifying new recombinant haplotypes and haplotype groupings, occur in YRI. Consequently, the Phase II HapMap provides increased resolution in the estimated fine-scale genetic map and improved power to detect and localize recombination hotspots (Fig. 2b).
