Fig. 2.

Comparison between the de novo assembly of the London strain (blue) and the Marseille strain (red) with the reference Y. pestis CO92. The inner links connect corresponding CARs in the reconstructions and the reference. Note that there is only a small inversion, marked in black among the grey links. The positions in both reconstructions covered by markers are indicated in green. All gaps that have IS annotations in the extant genomes are shown in orange. For CO92, all IS annotations are shown as well. In addition, gaps that are only partially filled or have very unconserved extant gap lengths are indicated in red. Finally, the outermost ring shows the mean read coverage in windows of length 200 bp in log scale. The figure was made with Circos [57].