Extended Data Fig. 10: Haplotype definition with IntroBlocker.

(a) Distribution of pairwise genetic distances in 5 Mb bins. Each subpanel shows the pairwise comparison of the haplotypes of one genome to the haplotypes of all other genomes. The distribution of pairwise distance revealed two major peaks (gray dashed line), one at 0.0095 variants per bp, and the other at 0.0145 variants per bp. A threshold of 0.011 was used to differentiate between these two peaks in IntroBlocker (red dashed line). (b) Graphical genotypes on chromosomes 2H and 4H. Regions of identical colors are assigned to the same haplotype at the chosen identity threshold (0.011). (c) Genetic distances between haplotypes of A40 and A42. Pairwise genetic distance between the haplotypes of A40 and A42 were plotted along the genome in 5 Mb windows.