Table 1. Strains used in this study.
| Strains | Characteristics | Source or reference | Code | Colour |
| M. tuberculosis H37Rv | M. tuberculosis human strain used extensively in laboratory research. From two separate laboratories. Genome sequenced. | AHVLA Weybridge CollectionRoyal Veterinary College | RvpRvv | Blue |
| M. tuberculosis Tb12 | Bangladeshi clinical isolate | Banu et al.(2004) | 12 | Purple |
| M. tuberculosis Tb30 | Bangladeshi clinical isolate | Banu et al.(2004) | 30 | Torquoise |
| M. tuberculosis Bj5208 | Beijing type clinical isolate | Brian Robertson, Imperial College; Martinez-Ganboa et al. (2008) | Bj | Green |
| M. bovis AF2122/97 | Genome sequenced strain, type 9, VNTR profile 8555*33.1 | Garnier et al. (2003) | 9b | Orange |
| M. bovis 61/0038/01 | Type 9, VNTR 6554*33.1 | AHVLA Weybridge Collection | 9a | |
| M. bovis 61/3558/00 | Type 9, VNTR 7524*33.1 | AHVLA Weybridge Collection | 9c | |
| M. bovis 61/1121/01 | Type 17, VNTR 7555*33.1 | AHVLA Weybridge Collection | 17a | Red |
| M. bovis 61/3139/06 | Type 17, VNTR 7455*33.1 | AHVLA Weybridge Collection | 17b | |
| M. bovis 21/7917/05 | Type 17, VNTR 7554*33.1 | AHVLA Weybridge Collection | 17c | |
| M. bovis 61/1307/01 | Type 35, VNTR 3354*33.1 | AHVLA Weybridge Collection | 35a | Brown |
| M. bovis 61/0507/01 | Type 35, VNTR 3354*33.1 | AHVLA Weybridge Collection | 35b |
The code is used in Figures 3 to 5, Table 2, Tables S1, S2, S3; S6, S7, S8, S9, S10, S11, S12, S13, S14 and Figure S6. In Figures S1, S2, S3, S4, S5, the human strains referred to in are H37Rv (from AHVLA Weybridge Collection), H37Rv DM (from the Royal Veterinary College) ; Bj5208 as H5208; the M. bovis strains abbreviated to the four figure part of their strain numbers. Elsewhere, as space permits, the full strain names are used. The colours are used in Figure 5 and 6, and Figures S6 and S7.