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.