Fig. 3

ML phylogenetic trees based on SNP concatenated sequence alignments of clinical isolates. ML phylogenetic trees of the 169 clinical isolates based on whole genome analysis. Radial rectangular tree layouts are shown for Lineages 1 (a), 2 (b) and 4 (c). Bootstrap values are shown in the phylogenetic trees. Clades show Lineage 2 Modern/typical (orange) and Ancestral/atypical (yellow). Scale bars indicate nucleotide substitutions per site. Black circles indicate foreign-born TB patients