Table 2.

dN/dS of the whole genes, T cell epitope regions and non-T cell epitope regions of 5 ppe genes with the highest homoplastic SNP density.

Gene	All Lineages			Lineage1 (n = 480)			Lineage2 (n = 521)			Lineage3 (n = 11)			Lineage4 (n = 158)
	Whole region	T cell epitope	non T cell epitope	Whole region	T cell epitope	non T cell epitope	Whole region	T cell epitope	non T cell epitope	Whole region	T cell epitope	non T cell epitope	Whole region	T cell epitope	non T cell epitope
Rv1196 (ppe18)	0.76	0.73	0.79	0.80	0.80	0.63	0.63	0.41	0.99	0.74	0.27	2.18	0.52	0.45	0.65
Rv1361c* (ppe19)	0.68	0.68	—	0.64	0.64	—	0.36	0.36	—	0.25	0.25	—	0.46	0.46	—
Rv3425* (ppe57)	0.60	0.60	—	0.38	0.38	—	1.31	1.31	—	0.38	0.38	—	0.76	0.76	—
Rv3429$ (ppe59)	1.80	0.00	1.79	2.14	0.00	2.13	1.40	0.00	1.38	0.00	0.00	0.00	1.22	0.00	1.20
Rv3478 (ppe60)	0.78	0.39	1.05	0.72	0.28	0.96	0.80	0.61	0.94	0.71	0.00	1.39	0.65	0.31	0.85

*PPE19 and PPE57 antigens had no non-T cell epitope regions so the dN/dS ratio was calculated only in the T cell epitope region.

^$No missense mutation occurred in the T cell epitope region of PPE59.