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Phylogenetic tree of 322Â M. tuberculosis strains isolated from TBM and PTB patients. The highlighted branches indicate the 108 strains in 47 terminal branch sets, together comprising the discovery set. The purple stars indicate the origin of the SNP in Rv0218 according to the ancestral reconstruction. The nucleotide for SNP position 261,869 is indicated next to the leaf labels. (PDF 60Â kb)

PE / PPE genes and drug resistance genes excluded for the phylogeny construction. Listed are the genes that were excluded from the multiple alignment used to create the phylogenetic tree. (DOCX 158Â kb)

Description of sequencing quality control parameters and statistics. Displayed are different measures of sequencing quality, used for the sequencing quality control check. (DOCX 208Â kb)

P-values of association between genes and TB disease phenotype in the discovery and validation sets. Scatterplot showing the p-values of the genes found in the discovery and the validation set. P-values in the discovery set are shown on the x-axis; p-values in the validation set are shown on the y-axis. Names are shown for genes significant in both the discovery and validation set. (DOCX 66Â kb)

Diagram demonstrating breseq calling a SNP in the PE-PGRS1 gene. Displayed are 60 Illumina sequencing reads mapping to the H37Rv reference genome (shown at the top and bottom). Visual inspection of the SNP confirms that it does not occur in a region containing uniformly lower base quality scores. (DOCX 1204Â kb)

[This corrects the article DOI: 10.1371/journal.pgph.0001788.]., (Copyright: © 2024 Du et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)