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fml12238-sup-0001-TableS1.pdfapplication/PDF537KTable S1. SNPs identified in the FJ05194 and GuangZ0019 isolates.
fml12238-sup-0002-FigS1.tifimage/tif1405KFig. S1. (A) Neighbour-joining phylogeny of 24 human Mycobacterium tuberculosis complex isolates based on 6586 high-quality SNP positions. The tree is rooted with Mycobacterium canettii. Branches are coloured according to the six main phylogeographical lineages of MTBC (Comas et al., 2010): pink, L1 lineage (the Philippines and the Indian Ocean Rim); blue, L2 lineage (East Asia); purple, L3 lineage (India, East Africa); red, L4 lineage (Europe, America); brown, L5, Mycobacterium africanum (West Africa 1); green, L6, M. africanum (West Africa 2). (B) Distribution of SNPs and drug resistance genes/IGRs in the two S-XDR genomes. The outer circle shows SNPs unique to FJ05197 and the inner circle shows those unique to GuangZ0019. Non-synonymous SNPs are represented by red bars, synonymous SNPs by blue bars and intergenic SNPs by yellow bars. The genes and intergenic regions labelled have previously been reported to be associated with drug resistance (Sandgren et al., 2009).

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