Fig. 2: Phasing results for the Lolium perenne genotype DH647.

a Reference-based phasing of the DH647 chromosomes (Chr) 1–7: track 1, pseudo-chromosomes of Kyuss, a doubled haploid progeny derived from anther culture of DH647, as reference. Vertical black segments indicate gaps in the Kyuss assembly; track 2, heatmap showing the density of SNPs phased by Hi-C; track 3, heatmap showing the density of all the SNPs phased by Hi-C and long reads in the chromosome-level phase block of DH647; track 4, dots represent small phase blocks that could not be integrated into the chromosome-level phase block; track 5, ratio of non-Kyuss alleles in the DH647 haplotype. Kyuss inherited one haplotype from DH647, and a high (red) or a low (blue) non-Kyuss allele ratio through the pseudo-chromosome suggests correct chromosome-level phasing. A middle ratio (gray) suggests low phasing quality, and the large segmental change of haplotype at the end of some pseudo-chromosomes indicate recombination events; track 6 and 7, heatmaps showing the density of SNPs called from haplome 1 and 2 of DH647 aligned against Kyuss, respectively. b Partition of Oxford Nanopore Technologies (ONT) reads from DH647 to haplotype 1 and 2 (blue and purple, respectively) using WhatsHap (left) and SortGrass (right). Gray indicates the percentage of unassigned reads. c ONT read alignment coverage in each DH647 haplome (H1 and H2). All DH647 ONT reads were aligned to the diploid assembly of DH647. Source data are provided as a Source Data file.