Fig. 4

Hi-C links between the two haplotypes after the gene binning step for the Pgt assembly. A Hi-C links within scaffold bins are excluded. The phasing signal in the Pgt assembly is clearly visible when phase switches are corrected. Over ~69 Mb of each haplotype have more than 80% of their Hi-C contacts to the same haplotype. In contrast, the presence of phase switches causes a noisier phasing signal between the haplotypes. BPgt contig tig00001281 with its associated haplotigs (black segments). The % of Hi-C trans contacts that link to haplotype A (with an associated smoothing line) are shown. Haplotigs are shown at the y coordinate that corresponds to their Hi-C contacts to haplotype A. This contig has a phase switch previously detected by parental data at ~2.062 Mb, which is also visible here with Hi-C data alone at the haplotig alignment boundary