Chinook salmon circos plot.

The interior links in the Circos plot, depict the duplicated (homeologous) blocks in the Chinook salmon genome defined by SyMAP. Only blocks larger than 2 million bp are shown. A) An illustration of the chromosomes with the centromere locations shown as blue filled circles (as defined by McKinney [33]). B) A scatterplot of the alignments between the McKinney [33] genetic map and the genome after filtering. The scale is in fractions of the total centimorgan length, with zero at the bottom and one at the top. C) A bar plot of the percent identity of the alignments between the blocks identified with SyMAP. The percent identity was weighted by alignment length and scored across million bp windows. The scale goes from 75 to 100 percent identity, and windows with greater than 90 percent identity were highlighted orange. D) A bar plot of the fraction of repetitive sequences found throughout the genome in million bp windows. The scale for this plot is from zero to one, with fractions of above 0.65 shown in orange.