Figure 4.

Genome composition of SPN, Lariey and other second pandemic plague genomes

(A) Sequence coverage at 207 gene loci involved in the pathogen virulence and transmission. Coverage represents the fraction of the gene CDS at least covered once (0 = not covered, 1 = fully covered).

(B) Non-synonymous (blue), synonymous (yellow) and intergenic (red) mutations present in a subset of 27 second pandemic ancient plague pMT1 plasmids. Open circles indicate sites not covered by at least 2 independent sequencing reads in an individual plasmid. The sequence data was trimmed and individual base quality scores rescaled in order to limit the potential impact of postmortem DNA damage.

(C) Same as Panel B, except that those mutations affecting the CO92 reference chromosome are shown.

See also Figure S6.