Fig. 5

Phylogenetic tree of 47 pairs of isolates from sequencing reads taken from the study of Bryant et al. Tips are labeled with the isolate number and its part of the pair (a or b), and are colored by its isolate classification as predicted by QuantTB. Isolates containing a mixed infection are colored in red. Isolates part of a reinfection pair are colored in blue. Isolates containing the H37Rv strain are colored in purple. Isolates containing antibiotic heterozygous (h) or homozygous (H) resistance mutations are in orange. All single infections isolates are colored in green. To the right of the mixed and reinfection isolates, we show the strains present in the isolate as predicted by QuantTB. Boxes are discussed in the main text