Fig. 3: Comparison of variants between sputum-culture pairs.

a Comparison of the amount of common and exclusive variants (Venn diagrams on the left) and comparison of frequency of variants in sputum (dWGS or eWGS) and culture (on the right). Colours represent common or exclusive variants. Percentage of MTB reads in the dWGS is shown above each plot. The complete figures containing the 61 pairs can be seen in Supplementary Fig. 4 and Supplementary Fig. 5. b Analysis of sputum-exclusive variants in this dataset and published ones. Percentage of pairs in each dataset with 0, 1-5 or more than 5 sputum-exclusive SNPs (all were not fixed variants). Colours represent the dataset. Abbreviations of countries/regions stand for: MZ-Mozambique, GE-Georgia, UK-United Kingdom, LIT-Lituania, SA-South Africa, VLC-Valencia (Spain). c Histogram of the difference of frequency (freq) between variants obtained in sputum versus culture (frequency in sputum - frequency in culture). Colours represent whether the variants are common or exclusive. Percentages of SNPs are shown on the top of the bars. The plot includes the percentage of SNPs that have a frequency difference equal to 0.Total number of variants is shown in grey boxes (n). d Differences of sputum-exclusive SNPs published in the original paper (in blue) versus the ones found by running our pipeline (in orange) for Goig et al.¹⁰ (upper panel) and Nimmo et al.¹⁶ (bottom panel) datasets. Source data are provided as a Source Data file.