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Additional file 1 of Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

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posted on 2020-12-21, 09:13 authored by Gary Napier, Susana Campino, Yared Merid, Markos Abebe, Yimtubezinash Woldeamanuel, Abraham Aseffa, Martin L. Hibberd, Jody Phelan, Taane G. Clark
Additional file 1: Table S1. The study samples (N=35,298) used and their lineages. Table S2. Robust barcoding SNPs (421 SNPs, including the 90 SNPs in Table S3). Table S3. The ninety minimal barcoding SNPs. Figure S1. Population structure of the Mycobacterium tuberculosis complex isolates by lineage. Figure S2. Examples of discrepancies using the 62-SNP barcode. Figure S3. The genome-wide distribution of barcoding SNPs (FST=1) for each lineage. Figure S4. Functional differences between genes containing lineage-barcoding (FST=1) SNPs. Figure S5. Differentiation of sub-lineages when comparing the 62- versus 90-SNP barcodes. Figure S6. The increased resolution of our 90-SNP barcode (implemented in TB-Profiler software) over the comparable (sub-)lineages of the SNP-IT tool.

Funding

Medical Research Council Medical Research Council (GB) Biotechnology and Biological Sciences Research Council NORAD and SIDA grants Foundation for the National Institutes of Health Bloomsbury SET

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    Genome Medicine

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    Keywords

    TuberculosisDiagnosticsProfilingSNPsBarcodingMycobacteria tuberculosis complex

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