Fig. 4.

Phylogeny of 20 diverse E. coli along with references used for benchmarking single-reference variant callers. The 20 E. coli under study are labelled as samples in the left-hand of three vertical label-lines. Phylogroups (clades) are labelled by color of branch, with the key in the inset. References were selected from RefSeq as being the closest to one of the 20 samples as measured by Mash, or manually selected from a tree (see “Methods”). Two assemblies from phylogroup B1 are in the set of references, despite there being no sample in that phylogroup