Figure 3

Core single-nucleotide polymorphism (SNP) phylogenetic analysis across 16 E. coli genomes (left), and comparison with the accessory genome (right). The Ortho_SNP_matrix.nex file created by SPANDx was directly imported into PAUP* 4.0 and used for phylogenetic construction based on 106,557 core SNPs. Using maximum parsimony, a tree with a consistency index of 0.78 was generated. The Bedcov_merge.txt file for presence/absence analysis of loci was automatically generated by SPANDx using the coverageBED module of BEDTools[6], based on the default 1 kb window size. Regions with <95% coverage across one or more genomes are displayed, representing ~1.6Mbp of the E. coli genome (x-axis). Coverage is shown as a heat map, with red lines equating to low or no coverage through to green lines, which represent uniform coverage at each 1 kb window. In combination, these tools enable facile visualisation of the core and accessory haploid genomes.