TB Profiler
This tool processes raw sequence data to infer strain type and identify known drug resistance markers.
A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.



This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.
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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).
Name: 5dc9314685a3f
Sample: 5dc9314685a3f

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Summary
ID: 5dc9314685a3f
Date: Mon Nov 11 10:02:23 2019
Strain: lineage2.2.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.57)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C0.978
rpoC764650c.1281G>T0.103
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.163
rrs1471900r.55c>t0.149
rrs1472106r.261g>a0.120
rrs1472137r.292g>a0.418
rrs1472150r.305t>a0.575
rrs1472151r.306c>t0.493
rrs1472160r.315c>t0.113
rrs1472172r.327t>c0.566
rrs1472203r.358g>a0.369
rrs1472210r.365a>c0.179
rrs1472214r.369c>g0.109
rrs1472225r.380c>a0.309
rrs1472235r.390g>c0.111
rrs1472240r.395g>a0.160
rrs1472242r.397c>t0.127
rrs1472251r.406g>a0.263
rrs1472259r.414c>a0.250
rrs1472338r.493a>g0.118
rrs1472344r.499c>t0.205
rrs1472379r.534t>c0.184
rrs1472400r.555c>t0.176
rrs1472422r.577t>c0.146
rrs1472507r.662c>g0.323
rrs1472513r.668t>c0.111
rrs1472517r.672t>a0.342
rrs1472518r.673g>t0.353
rrs1472530r.685g>a0.434
rrs1472537r.692c>t0.447
rrs1472544r.699c>a0.438
rrs1472545r.700a>t0.409
rrs1472549r.704g>a0.173
rrs1472557r.712g>a0.198
rrs1472566r.721g>a0.349
rrs1472571r.726g>c0.568
rrs1472573r.728c>t0.143
rrs1472579r.734g>t0.465
rrs1472581r.736a>t0.701
rrs1472584r.739a>t0.122
rrs1472598r.753a>c0.575
rrs1472599r.754g>t0.517
rrs1472612r.767g>t0.119
rrs1472616r.771g>a0.703
rrs1472655r.810g>a0.618
rrs1472658r.813g>a0.397
rrs1472660r.815t>c0.239
rrs1472661r.816a>g0.366
rrs1472670r.825g>t0.293
rrs1472673r.828t>g0.344
rrs1472675r.830t>c0.361
rrs1472677r.832c>t0.349
rrs1472690r.845c>a0.367
rrs1472697r.852t>c0.567
rrs1472713r.868t>c0.532
rrs1472716r.871c>t0.584
rrs1472742r.897c>t0.590
rrs1472744r.899a>g0.586
rrs1472781r.936c>t0.568
rrs1472793r.948a>t0.603
rrs1472803r.958t>a0.547
rrs1472895r.1050c>t0.528
rrs1472956r.1111t>c0.253
rrs1472957r.1112c>t0.219
rrs1472958r.1113a>g0.114
rrs1472973r.1128a>t0.303
rrs1472974r.1129a>g0.119
rrs1472987r.1142g>a0.104
rrs1472988r.1143t>c0.134
rrs1472990r.1145a>g0.329
rrs1473005r.1160c>t0.118
rrs1473035r.1190g>a0.377
rrs1473055r.1210c>t0.250
rrs1473056r.1211a>t0.283
rrs1473066r.1221a>g0.250
rrs1473081r.1236c>t0.107
rrs1473088r.1243a>g0.132
rrs1473093r.1248c>t0.113
rrs1473145r.1300c>t0.241
rrs1473148r.1303g>a0.163
rrs1473161r.1316a>c0.113
rrs1473163r.1318c>t0.176
rrs1473166r.1321g>a0.346
rrs1473177r.1332g>a0.475
rrs1473192r.1347a>g0.389
rrs1473199r.1354ca>c0.485
rrs1473205r.1360t>c0.392
rrs1473221r.1376c>t0.128
rrs1473252r.1407t>c0.268
rrs1473259r.1414c>t0.273
rrs1473276r.1431a>c0.229
rrs1473277r.1432g>a0.167
rrs1473301r.1456t>c0.154
rrs1473305r.1460g>t0.133
rrs1473316r.1471c>t0.277
rrs1473352r.1507c>t0.609
rrl1474218r.561t>a0.397
rrl1474228r.571t>c0.328
rrl1474249r.592g>t0.342
rrl1474252r.595t>a0.333
rrl1474351r.694g>t0.116
rrl1474353r.696a>g0.116
rrl1474355r.698a>g0.116
rrl1474362r.705a>g0.111
rrl1474387r.730c>t0.125
rrl1474488r.831g>t0.133
rrl1474516r.859c>a0.161
rrl1474537r.880g>a0.114
rrl1474638r.981c>g0.115
rrl1474734r.1077g>t0.122
rrl1474749r.1092c>t0.139
rrl1474760r.1103a>g0.167
rrl1474779r.1122g>a0.139
rrl1474782r.1125g>a0.139
rrl1474794r.1137c>t0.216
rrl1474823r.1166c>g0.184
rrl1474830r.1173a>g0.175
rrl1474831r.1174a>t0.139
rrl1474832r.1175a>t0.130
rrl1474864r.1207c>t0.268
rrl1474901r.1244a>g0.109
rrl1474904r.1247g>c0.224
rrl1474913r.1256t>c0.180
rrl1475129r.1472g>t0.133
rrl1475137r.1480a>g0.120
rrl1475154r.1497c>t0.120
rrl1475171r.1514c>t0.149
rrl1475175r.1518g>a0.120
rrl1475499r.1842c>t0.143
rrl1475515r.1858g>a0.152
rrl1475526r.1869c>a0.172
rrl1475531r.1874c>t0.156
rrl1475538r.1881t>a0.156
rrl1475539r.1882a>t0.147
rrl1475545r.1888t>g0.156
rrl1475548r.1891c>t0.212
rrl1475549r.1892t>c0.212
rrl1475686r.2029c>g0.158
rrl1475696r.2039t>c0.244
rrl1475699r.2042c>t0.220
rrl1475703r.2046a>g0.244
rrl1475715r.2058g>c0.125
rrl1475753r.2096c>g0.121
rrl1475777r.2120a>t0.167
rrl1475783r.2126t>g0.462
rrl1475803r.2146t>c0.580
rrl1475804r.2147g>c0.576
rrl1475816r.2159c>g0.570
rrl1475817r.2160a>g0.570
rrl1475858r.2201t>c0.510
rrl1475866r.2209t>a0.473
rrl1475881r.2224t>c0.106
rrl1475883r.2226a>c0.128
rrl1475898r.2241a>g0.267
rrl1475899r.2242g>a0.244
rrl1475916r.2259c>g0.231
rrl1475937r.2280a>t0.200
rrl1475943r.2286g>a0.286
rrl1475945r.2288c>a0.119
rrl1475952r.2295a>g0.308
rrl1475963r.2306g>t0.206
rrl1475970r.2313c>t0.258
rrl1475975r.2318c>t0.276
rrl1475977r.2320a>g0.300
rrl1475978r.2321c>t0.172
rrl1475988r.2331a>g0.250
rrl1475993r.2336c>t0.138
rrl1475997r.2340a>t0.185
rrl1475998r.2341c>t0.179
rrl1476001r.2344t>c0.207
rrl1476131r.2474c>t0.235
rrl1476164r.2507a>t0.113
rrl1476179r.2522c>t0.220
rrl1476194r.2537a>g0.208
rrl1476200r.2543a>t0.268
rrl1476201r.2544c>t0.161
rrl1476204r.2547c>t0.173
rrl1476207r.2550t>c0.113
rrl1476214r.2557g>t0.213
rrl1476215r.2558c>t0.191
rrl1476224r.2567a>g0.260
rrl1476251r.2594t>c0.116
rrl1476252r.2595t>g0.140
rrl1476256r.2599a>g0.178
rrl1476260r.2603a>g0.312
rrl1476280r.2623a>c0.180
rrl1476294r.2637a>g0.133
rrl1476295r.2638c>g0.114
rrl1476296r.2639c>t0.130
rrl1476311r.2654g>c0.140
rrl1476312r.2655t>c0.159
rrl1476313r.2656g>a0.118
rrl1476332r.2675g>c0.467
rrl1476338r.2681c>t0.490
rrl1476353r.2696g>t0.566
rrl1476358r.2701t>c0.640
rrl1476359r.2702c>g0.138
rrl1476369r.2712c>t0.527
rrl1476372r.2715t>c0.571
rrl1476381r.2724g>c0.128
rrl1476382r.2725a>g0.706
rrl1476383r.2726t>a0.677
rrl1476408r.2751g>a0.300
rrl1476411r.2754g>a0.169
rrl1476425r.2768g>t0.597
rrl1476428r.2771c>t0.745
rrl1476429r.2772a>c0.611
rrl1476463r.2806c>t0.133
rrl1476466r.2809c>t0.418
rrl1476481r.2824t>c0.756
rrl1476506r.2849t>c0.780
rrl1476513r.2856g>t0.120
rrl1476514r.2857c>t0.196
rrl1476515r.2858c>t0.278
rrl1476519r.2862c>g0.192
rrl1476524r.2867c>t0.318
rrl1476525r.2868a>g0.412
rrl1476530r.2873c>t0.192
rrl1476536r.2879g>a0.262
rrl1476538r.2881a>g0.233
rrl1476539r.2882a>g0.209
rrl1476540r.2883c>g0.244
rrl1476584r.2927c>t0.191
rrl1476585r.2928a>g0.159
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518871p.His253Tyr0.981
eis2714846p.Val163Ile1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.262
alr3841654c.-234A>C0.267
alr3841662c.-242A>G0.295
alr3841663c.-243G>A0.295
embC4242643c.2781C>T1.000
embA4243460c.228C>T0.966
embB4248115c.1602C>T1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

AnalysisProgram
Mappingbwa
Variant CallingBCFtools


Log

Drug Details
The estimated accuracy of drug resistance predictions is:

Drug1Sensitivity (%)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)
Pyrazinamide70.9 (62.4-79.4)93.9 (90.6-97.2)
Streptomycin87.1 (82.7-91.5)89.7 (86.0-93.4)
Ethionamide 73.6 (66.7-80.5)93.3 (89.6-97.0)
Moxifloxacin60.0 (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 acidNot determinedNot determined
Linezolid Not determinedNot determined
Clofazimine Not determinedNot determined
Bedaquiline Not determinedNot determined
Multi drug resistance91.2 (87.8-94.6)98.4 (97.2-99.6)
Extremely drug resistance75.9 (64.5-87.3)98.4 (97.3-99.5)

Lineages
Lineage2LocationStrainRD type
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.1.1.1Indo-OceanicEAI4;ZERORD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239
lineage1.1.3Indo-OceanicEAI6RD239
lineage1.2Indo-OceanicEAI1;EAI2RD239
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.2.2Indo-OceanicEAI1RD239
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.2East-Asian (Beijing)Beijing-RD142RD105;RD207;RD181;RD142
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.1East-African-IndianCAS1-KiliRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage3.1.2.1East-African-IndianCAS2RD750
lineage3.1.2.2East-African-IndianCASRD750
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage4.1.1.2Euro-American (X-type)X1None
lineage4.1.1.1Euro-American (X-type)X2RD183
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone
lineage4.2.2.1Euro-AmericanLAM7-TURNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.1Euro-American (LAM)LAM9None
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174
lineage4.3.2Euro-American (LAM)LAM3None
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None
lineage4.4.1.1Euro-AmericanS;OrphansNone
lineage4.5Euro-AmericanH;TRD122
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-American T2-UgandaRD724
lineage4.6.1.2Euro-AmericanT2RD724
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.1Euro-AmericanT3RD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.9Euro-American (H37Rv-like)T1None
lineage5West-Africa 1AFRI_2;AFRI_3RD711
lineage6West-Africa 2AFRI_1RD702
lineage7Lineage 7NoneNone
lineageBOVM. bovisBOV_1;BOV_2None

Citations
1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer
This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.
© 2019 London School of Hygiene and Tropical Medicine;