Extended Data Fig. 1: Genetic characteristics of M. tuberculosis complex strain.
From: Differential rates of Mycobacterium tuberculosis transmission associate with host–pathogen sympatry
a) Violin plot of the terminal branch lengths of the included Mtbc genetic lineages. The overlayed box plots display the median, the first and third quartile, and the horizontal lines represent the upper and lower values of the data. L1 = 523, L2widespread = 707, L2restricted = 75, L3 = 681, L4widespread = 2,494, L4restricted = 220, L5 = 17, L6 = 27 strains, respectively. b) Proportions of strains in clusters based on several different Single Nucleotide Substitution (SNS) thresholds by genetic lineage and site. L = Lineage, SNP = Single Nucleotide Polymorphism, NYC = New York City, NL = The Netherlands, HH = Hamburg, L2restricted includes sub-lineages 2.1., 2.2.2., and 2.2.1.1.2, L4restricted sub-lineages include 4.11, 4.2.1.1, 4.3.i2, 4.5, and 4.6.2.2. L2widespread refers to sub-lineages 2.2.1, 2.2.1.1, 2.2.1.1.1, 2.2.1.1.1i1, 2.2.1.1.1.i2, 2.2.1.1.1.i3, 2.2.1.2, L4 to all other L4 sub-lineages (see Methods).
