Figure 5.

(A) Number of core SNPs and (B) total number of SNPs identified in 30 emetic B. cereus group III strains isolated in association with a foodborne outbreak. Combinations of (A) five and (B) four reference-based variant calling pipelines and two reference genomes (either dustmasked or unmasked) were tested, along with one reference-free SNP calling method (kSNP3). Because the Parsnp pipeline reports core SNPs by definition, it was excluded from Figure 5B (total SNPs). For quantification of the total number of SNPs (Figure 5B), all sites with more than one unique character were counted.