Fig. 3

Example of a circular figure output. The figure was generated with Circleator using the example test dataset from the project website as input. It uses Neisseria meningitidis alpha14 (GenBank accession number: NC_013016) as a reference and depicts from outside to inside (1) complete genome (contigs of draft assemblies would be sorted by size); (2, 3) CDSs on forward and reverse strands; (4) core CDSs, defined as COGs that are shared between all input genomes; (5) unique CDSs that are only present in the reference genome (i.e. S. Typhimurium LT2 in this case); (6) unique SNPs, defined as being part of the core genome shared between all input genomes but containing a nucleotide in the reference genome that is different from all other input genomes; (7) G + C content in percent with maximum value shown as gray dotted line, calculated using non-overlapping windows of 5kbp length; and (8) GC skew, with maximum value shown as gray dotted line, calculated as (G - C) / (G + C) where G and C are nucleotide counts over non-overlapping windows of 5kbp length