Fig. 6

A contig with its associated haplotigs for each of the three Pt76 assemblies (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. If a haplotig has no Hi-C contacts, it is shown at at y = 100. A Contig tig00001246 from the Pgt assembly without phase switches and its associated haplotig alignment. Contig tig00001246 has on average 93.6% of its Hi-C contacts to haplotype A (indicated with red line), whereas the corresponding haplotig tig00001203_02 has 92.8% of its Hi-C contacts to haplotype B. No phase switches are present. B Contig tig00000828 from the HiFi-Canu assembly and its associated haplotig alignments. Contig tig00000828 appears to switch phase at ~1.5-3.7 Mb, which overlaps with the corresponding haplotig alignment start and end points. C Contig ptg000011l from the HiFi-hifiasm assembly and its associated haplotig alignments. Contig ptg000011l appears to switch phase at ~3–4.7 Mb and at ~5.8 Mb, which overlaps with the corresponding haplotig alignment start and end points. D Contig tig00000001 from the Nanopore assembly and its associated haplotig alignments. Distinct phase switch blocks such as in the HiFi assemblies are not visible. Collapsed regions where the Hi-C contacts are in the 50% range are clearly visible in the Nanopore assembly