Table 3 Comparison of all mixed infections, reinfection and relapses called between QuantTB and Bryant et al. Samples in bold are discordant between the two methods. QuantTB predictions also include the abundance levels of both strains identified within the sample. Samples labeled as Clinically TB negative on follow up were cases in which the second of the isolate pair assigned to the H37Rv strain by QuantTB, and tested negative for TB in the original study

Mixed (Lost a strain at later time point)

Sample 2: 81–18%

Sample 2

Sample 8: 53–47%

Sample 8

Sample 23: 60–40%

Sample 23

Sample 50: 75–25%

Sample 50

Mixed (Gained a strain at later time point)

Sample 42

Sample 45

Reinfection

Sample 10

Sample 10

Sample 14

Sample 14

Sample 35

Sample 35

Sample 15

Relapse

33 matching samples

33 matching samples

Sample 42

Sample 45

Sample 3

Clinically TB negative on follow up

Sample 36 (H37Rv)

Sample 36

Sample 37 (H37Rv)

Sample 37

Sample 38 (H37Rv)

Sample 38

Sample 3

Sample 15