SNP frequencies between (A) ESV1 and (B) EPV1 genotypes.

Frequencies were calculated using a sliding window and are expressed as a percentage of mismatching bases. The EPV1 genome is marked with a grey box showing the dominant genotype at each sampling point and the position of the H-NS gene is marked in bold. The position of the three H-NS binding sites in the EPV1 genome are marked with a black arrow underneath ORFs gp33, gp40 and gp48. The region of major divergence between the two EPV1 genotypes (shaded in grey) was not used in the calculation. Proposed transcriptional phases for each genome are labeled below as early, middle or late based on the presence of marker genes typically associated with the temporal classification of transcripts [55], [56]. A question mark indicates that the transcriptional phase was uncertain.