Fig. 3

Dot-plots showing alignments of re-assembled scaffolds by LDscaff versus chromosome-length scaffolds. Cutoff of 0.1 was used in a and c, cutoff of 0.2 was used in b and d. The panda reference chr17 and the horse reference chr10 are shown on the X axis in upper part and lower part, respectively. The Y axis shows the re-assembled scaffolds (alignment longer than 5000bp, percentage of match higher than 70%). They have been ordered and oriented to match the chromosomes as defined in the reference in order to facilitate comparison. Each dot represents the position of an individual resolved scaffold aligned to the reference. The color of the dots and lines were colored to represent the match rate for each scaffold (red indicate higher mat-ching rate, whereas blue indicates lower matching rate)