Fig. 2From: Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unitSNP phylogeny of the cluster 1 strains. The SNPs were called using SMALT and SAMtools to generate the VCF files which were filtered using VCFTools 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 and used to create a maximum likelihood phylogeny. The tree was rooted to midpoint. The red font colour indicates the reference strain. The scale bar indicates the rate of nucleotide differences per sequence siteBack to article page