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. 2021 Jun 30;11:13609. doi: 10.1038/s41598-021-92984-5

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© The Author(s) 2021

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Phylogenetic tree of 181 Da Nang strains (a) and 332 Hanoi strains (the northern Vietnam data set) (b), constructed using variants after mapping with H37Rv. Phylogenetic trees were constructed with the maximum likelihood method using RAxML version 8.2.8 (https://github.com/stamatak/standard-RAxML) and visualized with plotTree for python v2.7 (https://github.com/katholt/plotTree). Regions of difference (RDs), deletions, and SNVs in correlation with Mtb clades are depicted. Mtb Mycobacterium tuberculosis, SNV single nucleotide variant, Del deletion, aBJ ancient Beijing, mBJ modern Beijing, NA not available.