Figure 2: Example of manual scaffold editing based on linkage
map information
Example of manual repositioning of regions of the scaffolds from the
Hi-C step using information from the linkage map and male versus female
dot-plots. (A) ALLMAPS graphs for a male Hi-C scaffold showing position
of markers derived from male (orange) and female (green) mapping
population samples. Sections with crossing marker positions (left
subgraph) and negative slope (right subgraph) indicate regions in the
scaffold with orientation inconsistent with the linkage map. Sections in
right subgraph that are parallel but not collinear with the trend of the
curve indicate regions in the scaffold with ordering inconsistent with
the linkage map; (B) ALLMAPS graphs for a female Hi-C scaffold showing
position of markers derived from male and female mapping population
samples; (C) Dot-plot (mummerplot with data generated by NUCmer) of the
male and female Hi-C scaffolds. Blue arrows indicate the position and
orientation of the Chicago scaffolds that were inconsistent with linkage
map information. Black arrows indicate positional reordering of these
scaffolds, and red arrows indicate a flip of the scaffold; (D) ALLMAPS
graphs for the same male Hi-C scaffold after manual repositioning
showing consistency with the linkage map information; (E) ALLMAPS graphs
for the same female Hi-C scaffold after manual repositioning, showing
consistency with the linkage map information; (F) Dot-plot of the male
and female Hi-C scaffolds after manual repositioning, showing
consistency between sexes. Blue arrows demark the position and
orientation of the Chicago HiRise scaffolds after the manual
repositioning.