Fig. 2

Sputum samples under-represent the true genetic diversity of MTBC populations in the lung. We sequenced three samples from the enrollment time point of patient 12 and compared the detected population heterogeneity. a Mean frequency of detected v-SNPs across samples. Four v-SNPs affecting Rv0678 (mmpR) and ten v-SNPs affecting Rv3696c (glpK) are marked with red lines. b Detection pattern of v-SNPs across the three sputum samples. v-SNPs were classified as recurrent if they were detected in at least one sputum sample from a later time point. c Temporal detection pattern for listed v-SNPs across sputum samples isolated from patient 12 2, 4, 6, and 8 weeks post-enrollment. d Patterns of v-SNP temporal dynamics detected across all patients. One trajectory per type is highlighted for illustration purposes