MGY e14 phase variation. (A) ORF analysis of the phage e14 invertible locus. The invertase pinE resides next to the inverted locus (represented by a shaded rectangle). In the reverse orientation stfE is attached to ycfK, producing a longer ORF than in the forward variant (fusion of the red and green segments). ORFs in all figures were inferred using SnapGene® software (from GSL Biotech, Chicago, IL, USA). (B) Gap size distribution plotted against chromosomal position, centered on the e14 invertible locus. Two formations coexist at the same locus: a ribbon formation of normal reads (gray), and a funnel formation of abnormal reads (blue and green). The relative abundance of each formation represents the relative fraction of each genotype in the bacterial population. The IRs flanking the inversion are marked by orange rectangles (C) PCR confirmation of the coexistence of two genotypes. PCR was conducted on a single MGY colony with two sets of primers. Extracted genomic DNA was used as template for both sets (see Additional file 1 for description of primers). Each band represents the existence of one orientation in the population.