Fig. 3

Correlation analysis. a The correlation of all node pairs (nodes with dosage 1) in the 20 largest connected components as a function of the distance between nodes (in megabases). The 4830 dosage-1 nodes of the largest components account for 947.78 Mb. After removing pairs which had no valid correlation (NaN), 701,582 pairs remained in the dataset for plotting. b Reconstruction of the structure of chromosome 3 based on high correlation coefficients between nodes. Chromosome 3 is shown above, with the red block labeling the centromere as reported in the DMv6.1 annotation. The initial assembly consisted of three connected components and two additional contigs, which were manually placed at their approximate genomic location along the x-axis as determined by mapping the unitigs to DMv6.1 (the darker the color of a contig, the higher the maximum correlation to any other contig beyond its component). Contig pairs with the highest correlation (here denoted by the darkest color, representing a correlation coefficient of ≥ 0.8) could then be connected, revealing a more complete structure of the haplotype-resolved chromosome. The connected node pairs are marked by the dotted gray line