Figure 2.

Schematic diagrams for the three haplotype block criteria. Sites in strong LD with each other are indicated by the same color. The coverage criterion calculates the proportion of sequence that is contained in haplotype blocks, the “hole” criterion measures how often blocks are disrupted by internal SNPs not in LD with their neighbors, and the “overlapping blocks” criterion measures how ambiguous haplotype block boundaries are. In the bottom diagram, the black/green site is in strong LD with both black and green sites. See the “Material and Methods” and “Results” sections for more details.