Fig. 2: TP is associated with gene function and gene essentiality.

a Functional enrichment analysis of the 195 high-TP genes. Numbers in the dots represent the number of genes in each category. b Violin plots showing the TP profiles of genes in different functional categories, where “Insertion seqs and phages” has 73 genes, “Virulence, detoxification and adaptation” has 236 genes, “PE/PPE” has 160 genes, “Conserved hypotheticals” has 1007 genes, “Regulatory proteins” has 197 genes, “Lipid metabolism” has 268 genes, “Information pathways” has 238 genes, “Cell wall and cell processes” has 762 genes, and “Intermediary metabolism and respiration” has 918 genes. Error bars denote mean ± SD of TPs. The X-axis is presented on a log scale. c 1049 genes of the mycobacterial core-genome exhibit lower TPs than the other 2842 genes of the variable genome. Error bars represent mean ± SD of TPs. Statistical significance was assessed by the Wilcoxon test (two-sided). d TP comparison between 459 essential genes, 2874 non-essential genes, and 301 genes whose disruption confers growth advantage under axenic culture conditions. Statistical significance was assessed by the Wilcoxon test (two-sided); error bars represent mean ± SD of TPs. e Mtb Genes vulnerable to transcriptional perturbation exhibit low TPs. The horizontal black dashed line represents the maximum TP value of essential genes, and the vertical line shows the 5th percentile of vulnerability index of non-essential genes. The counts of essential and non-essential genes in each quadrant are displayed in green and yellow, respectively. f TP positively correlates with genes’ substitution rate, as simulated by genomegaMap (Wilson, 2020). Mean value and 95% credibility intervals of substitution rates are presented in colored points. Colored Lines depict the linear fit between TP and substitution rate. R and p represent Spearman’s correlation coefficient and the associated p values, respectively.