Figure 6.

Ranges of pairwise (A) core SNP differences and (B) total SNP differences between 30 emetic group III B. cereus group strains isolated in conjunction with a foodborne outbreak. Combinations of (A) five and (B) four reference-based variant calling pipelines and two reference genomes (either dustmasked or unmasked), as well as one reference-free SNP calling method (kSNP3) were tested. Lower and upper box hinges correspond to the first and third quartiles, respectively. Lower and upper whiskers extend from the hinge to the smallest and largest values no more distant than 1.5 times the interquartile range from the hinge, respectively. Points represent pairwise distances that fall beyond the ends of the whiskers. Because the Parsnp pipeline reports core SNPs by definition, it was excluded from Figure 6B (pairwise differences in total SNPs). For quantification of pairwise differences in the total number of SNPs (Figure 6B), all sites with more than one unique character were included.