Table 2.
Average CAI values for genes of different inferred relative time of insertion for the three query genomes
| S. typhi CT18 | S. paratyphi A SARB42 | S. typhimurium LT2 | |||
| Genes | CAI | Genes | CAI | Genes | CAI |
| PHA on branch 1 | 0.264 | PHA on branch 1 | 0.264 | PHA on branch 1 | 0.264 |
| PHA on branch 2 | 0.258 | PHA on branch 2 | 0.258 | PHA on branch 2 | 0.258 |
| PHA on branch 3 | 0.256 | PHA on branch 3 | 0.256 | PHA on branch 3 | 0.256 |
| PHA on branch 4[TS] | 0.221 | PHA on branch 4[TS] | 0.221 | PHA on branch 4[NTS] | 0.275 |
| PHA on branch 5[STY] | 0.283 | PHA on branch 5[SPA] | 0.297 | PHA on branch 5[STM] | 0.269 |
| PHA on branch CT18 | 0.282 | PHA on branch SARB42 | NA | PHA on branch LT2 | 0.307 |
| All genes | 0.310 | All genes | 0.315 | All genes | 0.313 |
| Ribosomal | 0.554 | Ribosomal | 0.560 | Ribosomal | 0.561 |
| tRNA synthetase | 0.437 | tRNA synthetase | 0.453 | tRNA synthetase | 0.434 |
Average CAI values for all genes in the genome, ribosomal protein coding and aminoacyl-tRNA synthetase genes, are also provided as a reference. Genes ≤300 bp were excluded. The reference gene set of highly expressed genes was the one proposed by Sharp and Li [49] using the genome of E. coli.