Fig. 5

A phylogenetic tree showing the placement of 53 metagenomic samples associated with the 2011 outbreak of E. coli O104:H4 [34]. Raw reads from each sample were mapped against the reference genome, K-12 W3110 [30], and all positions were called by GATK [15]. Filtered positions were then inserted into the E. coli phylogeny with the evolutionary placement algorithm (EPA) in RAxML [26]. The placement of the reference O104:H4 isolate, TY-2482, is shown in green, the reference genome is shown in gray, correctly genotyped samples are shown in red, while other genotyped E. coli isolates are shown in blue