Fig. 7

Single nucleotide polymorphism density and homoplasy density in Group I and Group II. a A map of SNP density and homoplasy density in Group I genomes. The outer ring displays the reference genome (C. botulinum strain Kyoto-F). Blue shaded regions indicate the core genome of Group I (only the core genome was considered for this analysis). The middle ring displays SNP density (SD), which is defined here as the number of parsimony informative SNPs found in 1 kb segments of the core genome. The inner ring displays the homoplasy density (HD), which is defined as the proportion of parsimony informative SNPs with a retention index below 0.5 for 1 kb segments of the core genome. b Histogram displaying the counts of 1 kb genome segments with homoplasy densities between 0 and 1 for Group I genomes. The vertical line indicates the median homoplasy density value. c A map of SNP and homoplasy density in Group II genomes. The outer ring displays information about the reference genome (C. botulinum strain Eklund 17B). Blue shaded regions indicate the core genome of Group II. The middle ring displays the SNP density and the inner ring displays the homoplasy density. d Histogram displaying the counts of 1 kb genome segments with homoplasy densities between 0 and 1 for Group II genomes. The vertical line indicates the median homoplasy density value. The figures suggest that SNPs and recombination are spread throughout the core genomes of each Group