Bacteria Genomic Inversion
It is easy to visualize genomic inversions with a syntenic dotplot. Since syntenic regions appear as colored lines in the syntenic dotplot generated by SynMap, inversions are seen when a syntenic line has a discontinuity or break, and there is an adjacent line with an opposite slope (e.g. a positively sloping line has a break and adjacent to it is a negatively sloping line).
In the example shown here, SynMap colored the syntenic lines green if they have a positive slope and red if they have a negative slope. This plot has a nearly continuous green line starting at the origin in the lower left and sloping to the upper right. While you will notice that this line does have some discontinuities that are the result of insertions, deletions, and duplications between the genomes, in the upper right area of the dotplot, you will see the green line break, and a red line start with the opposite slope. Beyond the red line is another green line. If you connect the two green lines, they will be almost perfectly inline with one another. The gap is completely filled by the red line. This offset red line is show that a genomic inversion happened in one of the two genomes.
