Fig. 1
From: Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
Phylogenetic reconstruction of the outbreak, as sequencing data were generated at three time points during the outbreak (corresponding to Panels a, b and c). The red node demonstrates the most frequently occurring SNP type. Node labels show the number of isolates of this type. Blue nodes are singletons. Edge labels show the number of SNPs between isolates. The turquoise node shows a cluster of two identical isolates from cases associated with a nursery. The header bar shows the date of the sequencing, the Illumina sequencing protocol used, the number of samples in the dataset and the total percentage of the S. Enteritidis reference genome which could be used for SNP calling (core genome). Subtle differences in the number of SNPs between nodes on the tree may be seen, for example in the unrelated nursery isolates (6 SNPs different between Panel a and Panel b). These differences are attributed to differences in core genome size, that is, the number of positions in the reference genome used to generate the results. The precise core genome size figures are shown as a percentage in the panel headings