Additional file 3 of Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations

Additional file 3: Figure S1. Changes of the distribution of Mycobacterium tuberculosis sub-lineages in Zhejiang Province (a) and five regions (b east, d west, e south, f north, g middle) from 1998 to 2013. c is the map of Zhejiang Province and the five regions. Figure S2. Phylogenetic tree of 197 Mycobacterium tuberculosis strains in China. Figure S3. Phylogenetic tree of 48 Mycobacterium tuberculosis strains in Zhejiang Province. Figure S4. Pairwise ratios of rates of nonsynonymous to synonymous substitutions (dN/dS) in sub-lineages in lineage 2 (a) and lineage 4 (b) for epitopes and non-epitope regions of T cell antigens. Wilcoxon rank-sum test was used to evaluated the differences of dN/dS between epitope and non-epitope regions of T cell antigens in each sub-lineage. Figure S5. Frequency distribution of the number of epitopes with nonsynonymous variants. A total of 491 T cell epitopes were included in the analysis. The number above each bar corresponds to the epitope count. a lineage 2, b lineage 4.