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Volume 25, Number 3—March 2019
Research

SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex

Samuel Lipworth1Comments to Author , Rana Jajou1, Albert de Neeling, Phelim Bradley, Wim van der Hoek, Gugu Maphalala, Maryline Bonnet, Elizabeth Sanchez-Padilla, Roland Diel, Stefan Niemann, Zamin Iqbal, Grace Smith, Tim Peto, Derrick Crook, Timothy Walker2, and Dick van Soolingen2
Author affiliations: University of Oxford, Oxford, UK (S. Lipworth, T. Peto, D. Crook, T. Walker); National Institute for Public Health and the Environment, Bilthoven, the Netherlands (R. Jajou, A. de Neeling, W. van der Hoek, D. van Soolingen); Wellcome Trust Centre for Human Genetics, Oxford (P. Bradley); National Reference Laboratory, Ministry of Health, Mbabane, Swaziland (G. Maphalala); Epicentre, Paris, France (M. Bonnet, E. Sanchez-Padilla); University of Kiel, Kiel, Germany (R. Diel); Borstel Research Centre, Borstel, Germany (S. Niemann); European Bioinformatics Institute, Cambridge, UK (Z. Iqbal); Public Health England, Birmingham, UK (G. Smith)

Main Article

Figure 2

Maximum-likelihood tree built from 70,144 informative positions from whole-genome sequences of all 323 Mycobacterium tuberculosis complex samples in the calibration set for the new SNPs to Identify TB tool. Lineages are of Mycobacterium tuberculosis. Red text denotes animal subspecies. BCG, bacillus Calmette–Guérin; SNP, single-nucleotide polymorphism.

Figure 2. Maximum-likelihood tree built from 70,144 informative positions from whole-genome sequences of all 323 Mycobacterium tuberculosis complex samples in the calibration set for the new SNPs to Identify TB tool. Lineages are of Mycobacterium tuberculosis. Red text denotes animal subspecies. BCG, bacillus Calmette–Guérin; SNP, single-nucleotide polymorphism.

Main Article

1These authors contributed equally to this article.

2Joint senior authors.

Page created: February 19, 2019
Page updated: February 19, 2019
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