Frequencies of genome-wide single nucleotide polymorphisms. Strains are from top to bottom IC11, Houston-1 and UGA10. Plot above each genome map indicate the frequency of SNPs unique to one strain, in a 20 kb window. On the Houston-1 genome map, green bars indicate sites of potential intra-gene recombination events, as detected by GENECONV. Orange bars indicate the position of genes for which the Ks-value is not the smallest for the pair of Houston-1 and IC11. On the IC11 and UGA10 genome maps, genes with atypically high Ks-values (Ks > 0.05) in the comparison of Houston-1 and the corresponding strain are marked with a pale blue bar. Horizontal dashed lines mark limit of the outliers of the distribution, i.e. the upper whisker of the SNP frequency distribution (percentile 75 + 1.5 times the interquartile distance). Numbers refer to segments that are outliers of the distribution. Genomic regions (dashed boxes) are indicated with the following abbreviations: BAP = Bartonella prophage; HGIa, HGIb, HGIc = genomic islands; ROR = run-off replication. The location of the T4SS virB and trw is shown with grey boxes.