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. 2020 May 15;10:8024. doi: 10.1038/s41598-020-64895-4

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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(a) The plots between the ratios of the numbers of homoplastic SNPs per total SNPs and the total SNPs of the 1,170 Mtb isolates. The ratios of homoplastic SNPs per total SNPs were markedly different between lineages so that the major groups from left to right are L4 (0.089 ± 0.011), L2 (0.130 ± 0.013), L3 (0.110 ± 0.006), and L1 (0.099 ± 0.015), respectively. The small leftmost group represents L4.8 which is most closely related to H37Rv, a member of L4.9. (b) The ratio of the number of homoplastic SNPs to total SNPs of each Mtb gene categorized into 8 functional categories: i) virulence and detoxification (VF, 226 genes), ii) lipid metabolism (LM, 238 genes), iii) information pathway (IP, 232 genes), iv) cell wall and cell process (CW, 751 genes), v) pe/ppe family protein (PE_PPE, 168 genes), vi) intermediary metabolism and respiration (IMR, 898 genes), vii) regulatory protein (RP, 193 genes), viii) conserved hypothetical protein (CHP, 1,163 genes). Each dot represents a gene that harbored at least a SNP. Statistical differences were evaluated with the nonparametric Kruskal-Wallis test. Asterisks (***) indicate the statistical significance (p < 0.001).