Figure 3: Assessment of MGE effects on ANI and AF between pairs of E. faecalis genomes.

The difference between unprocessed and mgecut processed genomes for A) ANI and B) AF estimates are shown. The dashed line in red indicates the median value. C) The relationship between ANI computed using unprocessed genomes and ANI computed using mgecut processed genomes where each point corresponds to a pair of genomes. The dashed blue line provides a one-to-one reference. Note, because ANI is symmetric while AF is not, there are twice as many genome pairs considered in panel B in comparison to panels A and C.