Fig. 5

Detection of the boundaries of inter-prophage deletion (indel-4) in Φ804–9/Φ804–10 present in FRIK1275 and FRIK1625. Short-read Illumina sequencing data from each strain was aligned to the nucleotide sequence of Φ804–9 and Φ804–10 from FRIK804. The difference in read coverage in FRIK1275 (dark green) and FRIK1625 (light green) relative to FRIK804 was determined at each location. Additionally, repeat sequences shared between Φ804–9 and Φ804–10 that were ≥ 100 bp (blue) were determined and mapped to identify potential sites of recombination. The difference in read coverage in ΔFRIK1275 and ΔFRIK1625 was below zero in the region of the deletion and terminated in direct repeats (shaded red) that flanked the deleted 47.7 kbp fragment. Predicted ORFs in Φ804–9 and Φ804–10 are shown in dark gray