Fig. 3

Alignment dot plots for the cow scaffolds on the Chromosome 1. Dot plots of alignment between benchmark results and trio-binned assembly for the cow scaffolds on the Chromosome 1. Each dot in the plot represents an alignment between benchmark results and the trio-binned assembly, and the color indicates the identity of the alignment. The upper left and lower right quadrants correspond to the scaffolds, which are color-coded according to their haplotypes. Red, blue, and gray correspond to maternal, paternal, and homozygous regions, respectively. The black dashed lines represent the boundaries of the scaffolds. a FALCON-Unzip + GreenHill result; b FALCON-Unzip + 3D-DNA result; c FALCON-Unzip + SALSA2 result