Figure 1 .
Comparative SNP analysis of five listerial strains From outside to inside: genome of L. monocytogenes 1/2a EGD-e colored according to COG categories (two strands shown separately). Number of SNPs normalized by gene length in the comparison of 1/2a EGD-e and L. innocua 6a CLIP11262, 1/2a EGD-e and 4a L99, 1/2a EGD-e and 4b CLIP80459, 1/2a EGD-e and 4b F2365, and the two 4b strains (4b F2365 and 4b CLIP80459). The innermost circle shows the location of phage genes (blue) and virulence genes (black) in the 1/2a EGD-e genome. Line graphs indicate the number of SNPs/gene length reflecting loci in the genome having a disproportionate number of SNPs. However, if a gene is specific to a certain genome, this will also be shown as a peak indicating a region of divergence within the two genomes under comparison. This analysis was performed using the MUMmer package  and SNPs were mapped to coding regions using PERL scripts. Data were visualized by GenomeViz . For each pairwise comparison of strains, percentage of SNPs per gene length of surface- and non-surface-associated genes, as well as the ratio of these values is given in the table. The latter was named “nucleotide divergence ratio” and denotes the relative amount of difference between those two classes of genes, in order to identify more (positive value) or less (negative value) abundant mutation in surface-associated than in non-surface-associated genes.
Hain et al. BMC Genomics 2012 13:144 doi:10.1186/1471-2164-13-144