Fig. 3 Associating plasmids with host genomes a) contact map b) proportion of interactions
To see if we could correctly associate plasmids even in extremely similar bacterial host genomes, we created a MetaPore-C contact map for a mock community with 6 bacterial strains and their plasmids (Fig. 3a). The community includes two E. coli strains, plus S. enterica, which shares >80% ANI with E. coli. The long regions of high contact density reveal the plasmid-genome contacts. There are small amounts of spurious, between-species interactions, due to ambiguous mapping between highly homologous regions. When the proportion of contacts is plotted for each possible plasmid-genome interaction, in every case the overwhelming majority of contacts is with the correct host genome (Fig. 3b).