TABLE 3.
A minimal set of 45 sSNPs that can be used to resolve M. tuberculosis and M. bovis isolates into the 56 sSNP types and 10 SNP cluster-subgroupsa
| ST | SCG | SNP position and allele in H37Rv
|
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 37031 | 43943 | 92197 | 220048 | 311611 | 519804 | 797736 | 909164 | 918314 | 923063 | 949219 | 1068149 | 1163132 | 1191859 | 1294396 | 1477596 | 1548147 | 1692067 | 1692683 | 1884695 | 1892015 | 1952599 | 2158580 | 2223680 | 2376133 | 2462869 | 2532614 | 2627946 | 2825579 | 2891265 | 2990037 | 3207247 | 3438383 | 3440461 | 3440539 | 3450722 | 3455683 | 3544707 | 3783054 | 4024270 | 4119243 | 4137829 | 4254003 | 4255919 | 4280708 | ||
| 1 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | A | A | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 2 | 3c | G | A | G | C | T | G | C | C | C | T | C | C | C | T | C | C | G | A | A | A | T | T | A | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 3 | 2 | G | A | G | C | T | G | T | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | G | G | T | C | A | G | G | A | C | C | T | G | C | T | C | T | G | A |
| 4 | 4 | G | A | G | C | T | G | C | C | C | A | C | C | C | T | C | C | G | A | A | A | T | T | A | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 5 | 4 | G | A | G | T | T | G | C | C | C | A | C | C | C | T | C | C | G | A | A | A | T | T | A | C | A | A | G | A | T | T | T | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 6 | 6a | G | A | T | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | T | C | A | G | G | A | T | G | T | G | C | T | C | G | A | G |
| 7 | 5 | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | T | G | T | G | C | T | C | G | G | G |
| 8 | 2 | G | A | G | C | T | G | T | T | T | T | C | C | C | T | C | T | G | G | C | G | C | C | G | G | G | A | A | G | G | T | C | A | G | G | A | C | C | T | G | C | T | T | T | G | A |
| 9 | 4 | G | A | G | T | T | G | C | C | C | A | C | C | C | T | C | C | G | A | A | A | T | T | A | G | A | A | G | A | T | T | T | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 10 | 2 | G | A | G | C | T | G | T | T | T | T | C | C | C | T | C | T | G | A | C | G | C | C | G | G | A | A | G | G | G | T | C | A | G | G | A | C | C | T | G | C | T | T | T | G | A |
| 11 | 2 | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | G | T | T | C | A | G | G | A | C | C | T | G | C | T | C | T | G | A |
| 12 | 6a | C | A | T | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | T | C | A | G | G | A | T | G | T | G | T | T | C | G | A | G |
| 13 | 6b | C | A | T | C | G | G | C | C | T | T | C | C | T | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | C | C | A | G | G | A | T | G | T | G | T | T | C | G | A | G |
| 14 | 6b | C | A | T | C | G | G | C | C | T | T | C | T | T | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | C | C | A | G | G | A | T | G | T | G | T | T | C | G | A | G |
| 15 | 1 | G | G | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | G | C | C | T | G | C | C | C | G | G | G |
| 16 | 7 | G | G | G | C | T | G | C | C | T | T | C | C | C | C | C | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | A | G | G | C | C | T | G | C | C | C | G | G | G |
| 17 | 2 | G | A | G | C | T | G | T | C | T | T | C | C | C | T | C | C | G | A | C | G | C | C | G | G | A | A | G | G | G | T | C | A | G | G | A | C | C | T | G | C | T | C | T | G | A |
| 18 | 6a | C | A | T | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | T | C | A | G | G | A | C | G | T | G | T | T | C | G | A | G |
| 19 | 2 | G | A | G | C | T | G | T | T | T | T | C | C | C | T | C | C | G | A | C | G | C | C | G | G | A | A | G | G | G | T | C | A | G | G | A | C | C | T | G | C | T | T | T | G | A |
| 20 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | T | G | C | T | C | G | G | G |
| 21 | 3a | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | G | T | T | C | A | G | G | A | C | C | T | G | C | T | C | T | G | G |
| 22 | 2 | G | A | G | C | T | G | T | T | T | T | C | C | C | T | C | T | G | A | C | G | C | C | G | G | G | A | A | G | G | T | C | A | G | G | A | C | C | T | G | C | T | T | T | G | A |
| 23 | 3a | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | G | T | T | C | A | G | G | A | C | C | T | G | C | T | C | G | G | G |
| 24 | 5 | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | T | C | A | G | G | A | T | G | T | G | C | T | C | G | G | G |
| 25 | 2 | G | A | G | C | T | G | T | C | T | T | C | C | C | T | C | C | G | A | C | G | C | C | G | G | A | A | G | G | G | T | C | A | G | G | A | C | C | T | G | C | T | T | T | G | A |
| 26 | 2 | G | A | G | C | T | G | C | T | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | G | T | T | C | A | G | G | A | C | C | T | G | C | T | C | T | G | A |
| 27 | 2 | G | A | G | C | T | G | T | T | T | T | C | C | C | T | C | T | G | A | C | G | C | C | G | G | A | A | G | G | G | T | C | A | G | G | A | C | C | T | G | C | T | C | T | G | A |
| 28 | 7 | G | G | G | C | T | G | C | C | T | T | C | C | C | C | C | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | T | A | G | G | C | C | T | G | C | C | C | G | G | G |
| 29 | 7 | G | G | G | C | T | A | C | C | T | T | C | C | C | C | T | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | T | A | G | G | C | C | T | G | C | C | C | G | G | G |
| 30 | 7 | G | G | G | C | T | A | C | C | C | T | C | C | C | C | T | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | T | A | G | G | C | C | T | G | C | C | C | G | G | G |
| 31 | 7 | G | G | G | C | T | A | C | C | T | T | C | C | C | C | T | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | T | G | G | G | C | C | T | G | C | C | C | G | G | G |
| 32 | 7 | G | G | G | C | T | A | C | C | T | T | C | C | C | C | T | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | T | G | G | G | C | G | T | G | C | C | C | G | G | G |
| 33 | 7 | G | G | G | C | T | A | C | C | T | T | C | C | C | C | T | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | T | G | G | G | C | G | T | G | C | T | C | G | G | G |
| 34 | 3b | G | A | G | T | T | G | C | C | T | A | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 35 | 3c | G | A | G | C | T | G | C | C | C | T | C | C | C | T | C | C | G | A | A | A | T | T | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 36 | 4 | G | A | G | C | T | G | C | C | C | A | C | C | C | T | C | C | G | A | A | A | T | T | A | G | A | A | G | A | T | T | T | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 37 | 1 | G | G | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | G | C | C | T | G | C | C | C | T | G | G |
| 38 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | A | A | T | T | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 39 | 4 | G | A | G | T | T | G | C | C | C | A | T | C | C | T | C | C | G | A | A | A | T | T | A | C | A | A | G | A | T | T | T | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 40 | 6b | C | A | T | C | G | G | C | C | T | T | C | T | T | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | C | C | A | G | T | A | T | G | T | G | T | T | C | G | A | G |
| 41 | 5 | G | A | G | C | T | G | C | C | T | T | C | C | C | C | C | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | T | G | T | G | C | T | C | G | G | G |
| 42 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | A | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 43 | 6b | C | A | T | C | G | G | C | C | C | T | C | T | T | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | C | C | A | G | G | A | T | G | C | G | T | T | C | G | A | G |
| 44 | 5 | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | A | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | T | G | T | G | C | T | C | G | G | G |
| 45 | 6a | C | A | T | C | T | G | C | C | C | T | C | C | C | C | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | T | C | A | G | G | A | T | G | T | G | T | T | C | G | A | G |
| 46 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | A | A | A | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 47 | 3b | G | A | G | C | T | G | C | C | C | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | G | C | T | C | G | G | G |
| 48 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 49 | 6a | C | A | T | C | T | G | C | C | T | T | C | C | C | T | C | C | A | A | C | G | T | C | G | G | A | G | G | A | T | T | C | A | G | G | A | T | G | T | G | T | T | C | G | A | G |
| 50 | 2 | G | A | G | C | T | G | T | C | T | T | C | C | C | T | C | C | A | A | C | G | T | C | G | G | A | A | G | G | G | T | C | A | G | G | A | C | C | T | G | C | T | C | T | G | A |
| 51 | 6b | C | A | T | C | G | G | C | C | T | T | C | T | T | T | C | C | A | A | C | G | T | C | G | G | A | G | G | A | T | C | C | A | G | T | A | T | G | T | G | T | T | C | G | A | G |
| 52 | 3b | G | A | G | C | T | G | C | C | C | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 53 | 4 | G | A | G | C | T | G | C | C | C | A | C | C | C | T | C | C | G | A | C | A | T | T | A | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 54 | 6b | C | A | T | C | G | G | C | C | T | T | C | T | C | T | C | C | G | A | C | G | T | C | G | G | A | G | G | A | T | C | C | A | G | G | A | T | G | T | G | T | T | C | G | A | G |
| 55 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | T | G | A | A | G | T | C | G | G | A | A | G | A | T | T | C | A | G | G | A | C | C | C | A | C | T | C | G | G | G |
| 56 | 3b | G | A | G | C | T | G | C | C | T | T | C | C | C | T | C | C | G | A | C | G | T | C | G | G | A | A | G | A | T | T | C | A | G | T | A | C | C | T | G | C | T | C | G | G | G |
a
ST, sequence type; SCG, SNP cluster group and subgroup.