Drug1 | Resistance | Supporting Mutations (frequency) |
Isoniazid | ||
Rifampicin | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
Ethionamide | ||
Fluoroquinolones | ||
Amikacin | ||
Capreomycin | ||
Kanamycin |
Lineage2 | Family | Main Spoligotype | RDS |
Gene | Chromosome Position | Mutation | Estimated fraction |
gyrB | 5452 | c.213G>A | 1.000 |
gyrB | 6454 | c.1215C>T | 1.000 |
gyrA | 7362 | p.Glu21Gln | 1.000 |
gyrA | 7585 | p.Ser95Thr | 1.000 |
gyrA | 7835 | c.534A>G | 0.987 |
gyrA | 8714 | c.1413A>G | 1.000 |
gyrA | 9143 | c.1842T>C | 1.000 |
gyrA | 9304 | p.Gly668Asp | 1.000 |
rpoB | 762689 | c.2883G>A | 1.000 |
rpoB | 763031 | c.3225T>C | 1.000 |
rpoC | 763375 | c.6C>A | 1.000 |
rpoC | 763660 | c.291T>C | 1.000 |
rpoC | 764134 | c.765C>G | 1.000 |
rpoC | 764152 | c.783C>T | 1.000 |
rpoC | 764159 | c.790C>T | 1.000 |
rpoC | 764278 | c.909A>G | 1.000 |
rpoC | 764287 | c.918C>T | 1.000 |
rpoC | 764293 | c.924G>A | 1.000 |
rpoC | 764365 | c.996C>T | 1.000 |
rpoC | 764405 | c.1036A>C | 1.000 |
rpoC | 764497 | c.1128A>G | 1.000 |
rpoC | 764506 | c.1137C>T | 1.000 |
rpoC | 764510 | c.1141C>T | 1.000 |
rpoC | 764521 | c.1152T>C | 1.000 |
rpoC | 764533 | c.1164C>T | 1.000 |
rpoC | 764536 | c.1167G>C | 1.000 |
rpoC | 764539 | c.1170C>G | 0.992 |
rpoC | 764554 | c.1185C>T | 1.000 |
rpoC | 764575 | c.1206T>G | 1.000 |
rpoC | 764578 | c.1209C>G | 1.000 |
rpoC | 764626 | c.1257C>T | 1.000 |
rpoC | 764632 | c.1263T>G | 0.993 |
rpoC | 764650 | c.1281G>C | 1.000 |
rpoC | 764651 | c.1282T>A | 1.000 |
rpoC | 764752 | c.1383G>C | 1.000 |
rpoC | 764761 | c.1392C>T | 1.000 |
rpoC | 765082 | c.1713G>A | 1.000 |
rpoC | 765220 | c.1851A>G | 1.000 |
rpoC | 765409 | c.2040T>C | 1.000 |
rpoC | 765478 | c.2109T>C | 1.000 |
rpoC | 765637 | c.2268C>G | 1.000 |
rpoC | 766010 | c.2641T>A | 1.000 |
rpoC | 766900 | c.3531T>C | 1.000 |
rpoC | 766945 | c.3576A>G | 1.000 |
rpoC | 767030 | c.3661C>T | 1.000 |
rpoC | 767062 | c.3693C>A | 1.000 |
Rv0678 | 779283 | c.294C>T | 1.000 |
Rv0678 | 779295 | c.306T>C | 1.000 |
Rv0678 | 779431 | p.Asn148Gln | 1.000 |
Rv0678 | 779452 | p.Gly155Arg | 1.000 |
Rv0678 | 779472 | c.483C>T | 1.000 |
rpsL | 781395 | c.-165T>C | 1.000 |
rpsL | 781875 | p.Gly106Ser | 1.000 |
rplC | 800946 | c.138T>C | 1.000 |
rplC | 801109 | p.Leu101Val | 1.000 |
embR | 1416222 | p.Phe376Leu | 0.223 |
embR | 1416234 | p.Cys372Gly | 0.253 |
embR | 1417294 | c.54T>C | 1.000 |
embR | 1417454 | c.-107C>A | 1.000 |
embR | 1417474 | c.-127C>T | 1.000 |
embR | 1417554 | c.-207C>G | 1.000 |
rrs | 1471845 | c.-1G>GT | 0.976 |
rrl | 1473403 | c.-255C>T | 1.000 |
rrl | 1473749 | r.92a>g | 1.000 |
rrl | 1474777 | r.1120t>c | 1.000 |
inhA | 1674816 | c.615T>C | 1.000 |
rpsA | 1833381 | c.-161T>C | 1.000 |
rpsA | 1834912 | c.1371A>G | 1.000 |
tlyA | 1917972 | c.33A>G | 1.000 |
katG | 2154724 | p.Arg463Leu | 1.000 |
katG | 2156055 | c.57G>A | 1.000 |
pncA | 2289104 | c.138T>C | 1.000 |
kasA | 2518132 | c.18C>T | 1.000 |
kasA | 2519287 | c.1173T>C | 1.000 |
eis | 2714628 | c.705T>G | 1.000 |
folC | 2746174 | c.1425T>G | 1.000 |
folC | 2746425 | p.Ala392Thr | 1.000 |
folC | 2746451 | p.Gly383Ala | 1.000 |
folC | 2747374 | c.225C>T | 1.000 |
folC | 2747549 | p.Val17Ala | 1.000 |
folC | 2747572 | c.27A>G | 1.000 |
folC | 2747575 | c.24C>G | 1.000 |
ribD | 2986929 | p.Leu31Phe | 1.000 |
thyX | 3067239 | p.Ala236Asp | 1.000 |
thyA | 3073782 | c.690T>C | 1.000 |
thyA | 3074160 | c.312T>C | 1.000 |
thyA | 3074238 | c.234G>A | 1.000 |
thyA | 3074247 | c.225G>A | 1.000 |
ald | 3086788 | c.-32T>C | 1.000 |
fbiA | 3640935 | c.393C>G | 1.000 |
alr | 3840527 | c.894T>G | 1.000 |
alr | 3841199 | c.222A>G | 1.000 |
alr | 3841419 | p.Val1Ala | 1.000 |
alr | 3841524 | c.-104G>A | 1.000 |
alr | 3841531 | c.-111A>G | 1.000 |
alr | 3841532 | c.-112A>G | 1.000 |
alr | 3841539 | c.-119C>T | 1.000 |
alr | 3841546 | c.-126C>G | 1.000 |
alr | 3841568 | c.-148G>A | 1.000 |
alr | 3841662 | c.-242A>G | 0.201 |
alr | 3841663 | c.-243G>A | 0.193 |
embC | 4240671 | p.Thr270Ile | 1.000 |
embC | 4242643 | c.2781C>T | 1.000 |
embA | 4243377 | p.Ser49Arg | 1.000 |
embA | 4243690 | p.Met153Thr | 1.000 |
embA | 4243919 | c.687G>A | 1.000 |
embA | 4244154 | p.Thr308Pro | 1.000 |
embA | 4244312 | c.1080T>G | 1.000 |
embA | 4245023 | c.1791A>G | 1.000 |
embA | 4245701 | c.2469G>T | 0.990 |
embB | 4246584 | p.Arg24Pro | 0.300 |
embB | 4247646 | p.Glu378Ala | 1.000 |
embB | 4248206 | p.Ser565Gly | 1.000 |
ethA | 4327546 | c.-73T>CT | 0.929 |
ethR | 4327830 | c.282C>T | 1.000 |
gid | 4407588 | c.615T>C | 1.000 |
gid | 4408185 | c.18G>A | 1.000 |
TBProfiler Version: 2.1.1
Analysis | Program |
Mapping | bwa |
Variant Calling | BCFtools |
Drug1 | Sensitivity (%) | Specificity (%) |
Isoniazid | 92.8 (89.9-95.7) | 100 (100-100) |
Rifampicin | 96.2 (93.9-98.5) | 98.1 (96.8-99.4) |
Ethambutal | 88.7 (83.6-93.8) | 81.7 (77.6-85.8) |
Pyrazinamide | 70.9 (62.4-79.4) | 93.9 (90.6-97.2) |
Streptomycin | 87.1 (82.7-91.5) | 89.7 (86.0-93.4) |
Ethionamide | 73.6 (66.7-80.5) | 93.3 (89.6-97.0) |
Moxifloxacin | 60.0 (29.6-90.4) | 68.7 (52.6-84.8) |
Ofloxacin | 85.5 (79.1-91.9) | 94.9 (91.8-98.0) |
Amikacin | 82.9 (74.4-91.4) | 98.3 (96.0-100) |
Capreomycin | 60.7 (50.6-70.8) | 90.7 (87.2-94.2) |
Kanamycin | 87.3 (81.3-93.3) | 93.4 (89.9-96.9) |
Para-aminosalisylic acid | Not determined | Not determined |
Linezolid | Not determined | Not determined |
Clofazimine | Not determined | Not determined |
Bedaquiline | Not determined | Not determined |
Multi drug resistance | 91.2 (87.8-94.6) | 98.4 (97.2-99.6) |
Extremely drug resistance | 75.9 (64.5-87.3) | 98.4 (97.3-99.5) |
Lineage2 | Location | Strain | RD type |
lineage1 | Indo-Oceanic | EAI | RD239 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 |
lineage1.1.1 | Indo-Oceanic | EAI4;EAI5 | RD239 |
lineage1.1.1.1 | Indo-Oceanic | EAI4;ZERO | RD239 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 |
lineage1.2 | Indo-Oceanic | EAI1;EAI2 | RD239 |
lineage1.2.1 | Indo-Oceanic | EAI2 | RD239 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 |
lineage2 | East-Asian | Beijing | RD105 |
lineage2.1 | East-Asian (non-Beijing) | None | None |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 |
lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 |
lineage2.2.1.2 | East-Asian (Beijing) | Beijing-RD142 | RD105;RD207;RD181;RD142 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 |
lineage3 | East-African-Indian | CAS | RD750 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 |
lineage3.1.1 | East-African-Indian | CAS1-Kili | RD750 |
lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 |
lineage3.1.2.1 | East-African-Indian | CAS2 | RD750 |
lineage3.1.2.2 | East-African-Indian | CAS | RD750 |
lineage4 | Euro-American | LAM;T;S;X;H | None |
lineage4.1 | Euro-American | T;X;H | None |
lineage4.1.2 | Euro-American (X-type) | T;H | None |
lineage4.1.2.1 | Euro-American (X-type) | T1;H1 | RD182 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None |
lineage4.1.1.2 | Euro-American (X-type) | X1 | None |
lineage4.1.1.1 | Euro-American (X-type) | X2 | RD183 |
lineage4.1.1.3 | Euro-American (Haarlem) | X1;X3 | RD193 |
lineage4.2 | Euro-American | H;T;LAM | None |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None |
lineage4.2.2.1 | Euro-American | LAM7-TUR | None |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None |
lineage4.3.1 | Euro-American (LAM) | LAM9 | None |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None |
lineage4.3.2.1 | Euro-American (LAM) | LAM3 | RD761 |
lineage4.4 | Euro-American | S;T | None |
lineage4.4.2 | Euro-American | T1;T2 | None |
lineage4.4.1 | Euro-American (S-type) | S;T | None |
lineage4.4.1.2 | Euro-American | T1 | None |
lineage4.4.1.1 | Euro-American | S;Orphans | None |
lineage4.5 | Euro-American | H;T | RD122 |
lineage4.6 | Euro-American | T;LAM | None |
lineage4.6.1 | Euro-American (Uganda) | T2 | RD724 |
lineage4.6.1.1 | Euro-American | T2-Uganda | RD724 |
lineage4.6.1.2 | Euro-American | T2 | RD724 |
lineage4.6.2 | Euro-American | T;LAM | RD726 |
lineage4.6.2.1 | Euro-American | T3 | RD726 |
lineage4.6.2.2 | Euro-American (Cameroon) | LAM10-CAM | RD726 |
lineage4.7 | Euro-American (mainly T) | T1;T5 | None |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None |
lineage5 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 |
lineage6 | West-Africa 2 | AFRI_1 | RD702 |
lineage7 | Lineage 7 | None | None |
lineageBOV | M. bovis | BOV_1;BOV_2 | None |