Extended Data Fig. 5: Comparison of haplotype sequences within linkage groups 1 (a) and 2 (b).

Each of the four horizontal rows represents a haplotype of the chromosome (Hera 1, Hera 2, Stieglitz 1 and Stieglitz 2). For each haplotype, three types of information are within each box, top: IBD and unique regions along the chromosome (at 50 kb resolution), middle: distribution of SNPs at IBD regions, and bottom: scaffolded contigs. For each chromosome, three pairwise structural comparisons are shown highlighting inversions (orange), duplications (blue), translocations (green) and syntenic regions (gray). Note that all the regions involving the breakpoints of the SVs ended within contigs. IBD regions can be shared by two (dip), three (trip) or even four (tetrap) haplotypes. The x-axis scale: 0–100 Mb.