Table S1. Primers. Table S2. Prophages and phages used to construct the end sequence profiling index. Table S3. E. coli genomes used in phylogenetic tree construction. Table S4. SNPs unique to 95NR1 and 95JB1. Table S5. Genes outside of annotated prophages of 11128 to which reads of 95NR1 and 95JB1 do not align. Table S6. Identification of phage insertion sites of 95NR1 and 95JB1 and associated phage terminal regions using paired-end reads. Fig. S1. Mapping of 95NR1 and 95JB1 reads to plasmids pO111_2 to pO111_5 of 11128. Fig. S2. Stx2-converting phage PCRs performed in this study.
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