Fig. 2

SNP phylogeny of C. sakazakii strains belonged to ST13. The SNPs werecalled using SMALT and SAMtools to generate the VCF files which were filtered usingVCFTools to include only SNPs with minimum quality score of 30, minimum depth of 8,and minimum allele frequency of 0.90. The SNPs in the cluster were concatenated andused to create a maximum likelihood phylogeny. The tree was rooted to midpoint. C.sakazakii CS-1 was the reference strain. The scale bar indicates the rate of nucleotidedifferences per sequence site