Fig. 2

Plot of phylogeny (left) against recombinations predicted by Gubbins and SNP density. The reference genome of S26/3 is shown as an orange line with predicted CDSs in the forward and reverse frames shown in light blue above and below this line. Above this is the SNP density plotted with a window size of 1 kb. Peaks at CAB255 (putative membrane protein), CAB381 (pmp13G) and CAB596 (pmp16G), the sites of recombination, can be seen. These recombination events were the only ones identified by Gubbins. Figure was drawn using Phandango