Figure 1.

Diagram of the FGT and haplotype block identification. A, Consider two loci A and B, each with two alleles (denoted as A₁, A₂, B₁, and B₂). On the left, only three gametes (A₁B₁, A₁B₂, and A₂B₁) are observed between loci A and B (which arise from mutations; suppose A₁B₁ is the wild type). On the right, recombination has occurred between A₁B₂ and A₂B₁ haplotypes, which leads to all four gametes being observed in a sample. B, Haplotype block identification. The FGT is conducted between pairwise loci, and 0 and 1 denote the absence and presence, respectively, of all four gametes between locus pairs. In this example with eight loci, three haplotype blocks were identified, with the first block including SNPs 1, 2, and 3; the second block including SNPs 4, 5, and 6; and the last block including SNPs 7 and 8.