TABLE 2.
Diversity of SNP genotyping patterns between M. tuberculosis strains causing PTB and EPTB
| SCG | ST | No. of PTB cases (%) | No. of EPTB cases (%) | SNP profilea |
|---|---|---|---|---|
| 1 | 15 | 506 (39.9) | 47 (35.6) | GGGCTGCCTTCCCTCCGACGTCGGAAGATTCAGGGCCTGCCCGGG |
| Th1 | 1 (0.1) | 0 (0.0) | ...T......................................... | |
| Th2 | 3 (0.2) | 0 (0.0) | ...........................G................. | |
| 2 | 3 | 20 (1.6) | 0 (0.0) | .A....T....................GG.....A.....T.T.A |
| 8 | 4 (0.3) | 2 (1.5) | .A....TT.......T.G..C...G.AGG.....A.....TTT.A | |
| 10 | 179 (14.1) | 42 (31.8) | .A....TT.......T....C......GG.....A.....TTT.A | |
| 11 | 1 (0.1) | 0 (0.0) | .A.........................G......A.....T.T.A | |
| 19 | 176 (13.9) | 9 (6.8) | .A....TT............C......GG.....A.....TTT.A | |
| 22 | 70 (5.5) | 14 (10.6) | .A....TT.......T....C...G.AGG.....A.....TTT.A | |
| 25 | 39 (3.1) | 0 (0.0) | .A....T.............C......GG.....A.....TTT.A | |
| 26 | 10 (0.8) | 2 (1.5) | .A.....T...................G......A.....T.T.A | |
| F | 0 (0.0) | 1 (0.8) | .A....T........T....C......GG.....A.....TTT.A | |
| K | 50 (3.9) | 1 (0.8) | .A....TT...................GG.....A.....T.T.A | |
| Th3 | 1 (0.1) | 0 (0.0) | .A....TT...................GG.....A.....TTT.A | |
| Th4 | 1 (0.1) | 0 (0.0) | .A....TT.....C......C......GG.....A.....TTT.A | |
| Th5 | 2 (0.2) | 0 (0.0) | .A....TT.......T....C.....AGG.....A.....TTT.A | |
| 3a | 21 | 22 (1.7) | 0 (0.0) | .A.........................G......A.....T.T.. |
| 3b | 20 | 12 (0.9) | 2 (1.5) | .A................................A.....T.... |
| 34 | 7 (0.6) | 2 (1.5) | .A.T.....A........................A..CA.T.... | |
| 3c | Th6 | 1 (0.1) | 0 (0.0) | .A.T....CA...........TA...........A..CA.T.... |
| 4 | 9 | 1 (0.1) | 0 (0.0) | .A.T....CA.........A.TA...........A..CA.T.... |
| 5 | 7 | 47 (3.7) | 3 (2.3) | .A................................ATG...T.... |
| 24 | 103 (8.1) | 6 (4.5) | .A.......................G........ATG...T.... | |
| 41 | 1 (0.1) | 0 (0.0) | .A...........C...........G........ATG...T.... | |
| Th7 | 1 (0.1) | 0 (0.0) | .A...................T............ATG...T.... | |
| Th8 | 1 (0.1) | 0 (0.0) | .A.......................G.G......ATG...T.... | |
| Th9 | 3 (0.2) | 0 (0.0) | .A.......................G........ATG........ | |
| 6a | 18 | 7 (0.6) | 1 (0.8) | CAT......................G........A.G..TT..A. |
a
The dot indicates that the nucleotide is identical to that in the reference sequence.