Extended Data Fig. 2: Completeness and accuracy validation of chromosome arms and centromeres in the Jin668 genome.
a, Assessment of the Jin668 genome assembly using LTR Assembly Index (LAI). The x-axis lists chromosomes and y-axis represents LAI values. The red dashed line represents the mean value. b,c, Hi-C map of the Jin668 genome showing genome- and chromosome-wide all-by-all interactions. d, Bionano de novo assembly contigs were mapped to the Jin668 reference assembly. e, The distribution of QV values calculated from Merqury and Merfin on different chromosomes. f, The distribution of different types of unique k-mers along the centromeric regions in chromosomes of Jin668. Each bar shows the number of different types of k-mers in a bin of length 20 Kb. The blue bars represent single-clump k-mers, which suggest a good base-level quality. While the orange (multiple-clumps) and green (no-clumps) bars suggest a low base-level quality in the region. The x-axis unit is megabases (Mb), and the y-axis represents values multiplied by 10³. g, NucFreq plot of centromeric regions in chromosomes of Jin668. HiFi coverage depth (black) along with secondary allele frequency (red) for all centromeres and surrounding regions. The x-axis represents chromosome positions in megabases (Mb), and the y-axis shows HiFi depth, ranging from 0 to 100.
