Table 2 Average CAI values for genes of different inferred relative time of insertion for the three query genomes

From: Genetic flux over time in the Salmonella lineage

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.

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