Table 1. Consensus mutations in all HT-sequenced samples.
| Gene(s) affected | Genome position | Mutation | Annotation | Function(s) of related gene(s) |
| ylbE_1 | 547 694 | A→G | Pseudogene | Predicted protein |
| ylbE_1 | 547 835 | +G | Pseudogene | Predicted protein |
| flhD/uspC | Δ1 976 527–1 977 302 | IS1 deletion | Intergenic | Subunit of flagella regulator (FlhD2C2)/universal stress protein |
| rrlD | 3 422 257–3 422 259 | ATC→CAT | Non-coding | 23S rRNA |
| ppiC/yifO | 3 957 957 | C→T | Intergenic | Peptidyl-prolyl cis-trans isomerase C/conserved protein |
| gltP/yjcO | 4 294 291 | T→C | Intergenic | Glutamate and aspartate DAACS transporter/conserved protein |
| gltP/yjcO | Δ4 294 305–4 294 415 | Δ111 bp | Intergenic | Glutamate and aspartate DAACS transporter/conserved protein |