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: 5dd3b17ec74ac
Sample: 5dd3b17ec74ac

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Summary
ID: 5dd3b17ec74ac
Date: Tue Nov 19 09:13:13 2019
Strain: lineage4.6.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
RifampicinRrpoB p.His445Asn (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB762983c.3177C>T0.132
rpoC764566c.1197C>G0.190
rpoC764575c.1206T>C0.222
rpoC764581c.1212T>C0.294
rpoC764582p.Leu405Met0.286
rpoC764605c.1236G>C0.293
rpoC764611c.1242G>C0.250
rpoC764620c.1251G>T0.156
rpoC764632c.1263T>C0.233
rpoC764641c.1272C>T0.209
rpoC764644c.1275G>C0.214
rpoC764650c.1281G>T0.233
rpoC764705p.Leu446Lys0.149
rpoC764719c.1350G>A0.128
rpoC764953c.1584G>C0.191
rpoC764958p.Glu530Ala0.200
rpoC764964p.Phe532Tyr0.152
rpoC764968c.1599T>C0.250
rpoC764989c.1620G>A0.157
rpsL781395c.-165T>C1.000
rrs1471876r.31g>a0.238
rrs1471892r.47g>a0.264
rrs1471893r.48t>g0.264
rrs1472106r.261g>a0.312
rrs1472108r.263c>a0.316
rrs1472151r.306c>t0.136
rrs1472153r.308g>a0.143
rrs1472160r.315c>t0.361
rrs1472164r.319g>a0.260
rrs1472172r.327t>c0.695
rrs1472177r.332c>t0.278
rrs1472181r.336g>a0.352
rrs1472214r.369c>g0.745
rrs1472225r.380c>a0.313
rrs1472235r.390g>c0.664
rrs1472240r.395g>c0.632
rrs1472242r.397c>t0.639
rrs1472251r.406g>a0.438
rrs1472253r.408g>t0.432
rrs1472259r.414c>a0.438
rrs1472266r.421c>a0.410
rrs1472277r.432c>g0.303
rrs1472338r.493a>c0.378
rrs1472344r.499c>t0.628
rrs1472349r.504a>t0.500
rrs1472350r.505c>t0.265
rrs1472373r.528g>a0.311
rrs1472374r.529t>a0.545
rrs1472379r.534t>g0.390
rrs1472382r.537g>t0.578
rrs1472389r.544g>a0.280
rrs1472390r.545t>a0.276
rrs1472391r.546c>t0.701
rrs1472412r.567a>c0.610
rrs1472415r.570t>g0.565
rrs1472530r.685g>a0.217
rrs1472537r.692c>t0.235
rrs1472544r.699c>a0.224
rrs1472545r.700a>g0.224
rrs1472547r.702g>a0.183
rrs1472557r.712g>a0.358
rrs1472591r.746g>a0.295
rrs1472598r.753a>t0.726
rrs1472616r.771g>a0.759
rrs1472697r.852t>c0.244
rrs1472713r.868t>c0.213
rrs1472714r.869a>t0.426
rrs1472715r.870c>g0.536
rrs1472716r.871c>a0.536
rrs1472734r.889c>t0.442
rrs1472741r.896g>a0.389
rrs1472742r.897c>t0.776
rrs1472754r.909g>t0.358
rrs1472781r.936c>t0.783
rrs1472793r.948a>t0.774
rrs1472803r.958t>a0.753
rrs1472812r.967a>c0.435
rrs1472887r.1042g>c0.700
rrs1472936r.1091c>t0.412
rrs1472956r.1111t>c0.443
rrs1472957r.1112c>t0.455
rrs1472958r.1113a>t0.479
rrs1472959r.1114t>a0.479
rrs1472963r.1118g>a0.500
rrs1472982r.1137g>c0.542
rrs1472987r.1142g>t0.549
rrs1472988r.1143t>a0.549
rrs1472989r.1144g>a0.527
rrs1472990r.1145a>g0.520
rrs1473002r.1157g>t0.532
rrs1473004r.1159t>a0.525
rrs1473008r.1163c>a0.539
rrs1473009r.1164t>c0.558
rrs1473038r.1193a>c0.331
rrs1473044r.1199c>g0.766
rrs1473051r.1206t>c0.581
rrs1473053r.1208t>g0.585
rrs1473056r.1211a>t0.566
rrs1473062r.1217t>a0.582
rrs1473068r.1223a>g0.532
rrs1473080r.1235c>t0.437
rrs1473088r.1243a>g0.388
rrs1473093r.1248c>t0.368
rrs1473097r.1252g>c0.362
rrs1473099r.1254t>a0.369
rrs1473163r.1318c>t0.462
rrs1473164r.1319c>g0.479
rrs1473173r.1328c>t0.285
rrs1473177r.1332g>a0.664
rrs1473192r.1347a>g0.281
rrs1473193r.1348g>a0.237
rrs1473199r.1354ca>c0.700
rrs1473202r.1357c>t0.658
rrs1473204r.1359c>t0.268
rrs1473205r.1360t>c0.280
rrs1473352r.1507c>g0.541
rrs1473353r.1508c>g0.536
rrs1473358r.1513g>c0.532
rrs1473359r.1514g>c0.527
rrl1473922r.265a>c0.288
rrl1474199r.542g>a0.217
rrl1474201r.544t>c0.221
rrl1474202r.545t>a0.221
rrl1474218r.561t>a0.350
rrl1474228r.571t>c0.333
rrl1474235r.578g>c0.301
rrl1474249r.592g>t0.313
rrl1474252r.595t>a0.289
rrl1474264r.607t>g0.321
rrl1474265r.608g>a0.321
rrl1474558r.901g>c0.321
rrl1474584r.927c>g0.381
rrl1474586r.929t>a0.373
rrl1474587r.930g>a0.325
rrl1474602r.945c>g0.321
rrl1474828r.1171g>c0.276
rrl1474844r.1187g>t0.297
rrl1474864r.1207c>t0.241
rrl1474866r.1209c>a0.216
rrl1474869r.1212g>t0.447
rrl1474875r.1218g>a0.434
rrl1474876r.1219t>a0.434
rrl1474883r.1226t>c0.264
rrl1475154r.1497c>a0.167
rrl1475171r.1514c>a0.140
rrl1475175r.1518g>a0.140
rrl1475499r.1842c>g0.230
rrl1475517r.1860c>t0.368
rrl1475518r.1861a>g0.361
rrl1475526r.1869c>t0.400
rrl1475538r.1881t>c0.379
rrl1475539r.1882a>t0.368
rrl1475540r.1883c>t0.368
rrl1475545r.1888t>g0.347
rrl1475553r.1896g>t0.230
rrl1475555r.1898t>g0.333
rrl1475564r.1907c>a0.245
rrl1475571r.1914a>t0.269
rrl1475574r.1917c>g0.269
rrl1475575r.1918c>a0.259
rrl1475576r.1919c>a0.269
rrl1475577r.1920c>g0.252
rrl1475589r.1932g>a0.262
rrl1475672r.2015c>t0.250
rrl1475673r.2016t>c0.255
rrl1475685r.2028t>g0.255
rrl1475687r.2030c>t0.255
rrl1475688r.2031g>c0.255
rrl1475697r.2040c>a0.321
rrl1475702r.2045g>t0.316
rrl1475707r.2050t>c0.339
rrl1475713r.2056c>g0.317
rrl1475716r.2059a>t0.274
rrl1475735r.2078t>c0.323
rrl1475791r.2134a>g0.350
rrl1475803r.2146t>c0.653
rrl1475804r.2147g>c0.655
rrl1475816r.2159c>g0.701
rrl1475817r.2160a>g0.714
rrl1476141r.2484a>g0.484
rrl1476153r.2496t>c0.508
rrl1476154r.2497g>t0.317
rrl1476160r.2503t>g0.183
rrl1476164r.2507a>g0.517
rrl1476165r.2508t>a0.517
rrl1476252r.2595t>g0.548
rrl1476260r.2603a>g0.576
rrl1476266r.2609g>a0.586
rrl1476279r.2622g>t0.257
rrl1476280r.2623a>c0.278
rrl1476281r.2624t>a0.278
rrl1476293r.2636c>t0.270
rrl1476294r.2637a>g0.270
rrl1476295r.2638c>g0.286
rrl1476296r.2639c>t0.286
rrl1476301r.2644a>t0.294
rrl1476311r.2654g>c0.325
rrl1476312r.2655t>c0.325
rrl1476313r.2656g>a0.361
rrl1476336r.2679c>t0.603
rrl1476356r.2699c>g0.540
rrl1476357r.2700t>a0.540
rrl1476358r.2701t>c0.638
rrl1476359r.2702c>g0.256
rrl1476369r.2712c>t0.239
rrl1476381r.2724g>c0.239
rrl1476382r.2725a>g0.634
rrl1476383r.2726t>g0.269
rrl1476384r.2727g>t0.654
rrl1476404r.2747g>a0.346
rrl1476408r.2751g>a0.737
rrl1476411r.2754g>a0.371
rrl1476425r.2768g>a0.387
rrl1476429r.2772a>c0.371
rrl1476442r.2785t>a0.712
rrl1476443r.2786g>t0.730
rrl1476455r.2798c>a0.705
rrl1476456r.2799a>t0.684
rrl1476463r.2806c>t0.421
rrl1476466r.2809c>t0.749
rrl1476470r.2813c>t0.305
rrl1476474r.2817c>t0.270
rrl1476481r.2824t>c0.289
rrl1476506r.2849t>c0.664
rrl1476565r.2908g>a0.159
rrl1476566r.2909a>g0.160
rrl1476567r.2910c>t0.400
rrl1476573r.2916a>t0.250
rrl1476575r.2918c>t0.250
tlyA1917972c.33A>G1.000
katG2155389c.723G>C1.000
thyX3067474p.Pro158Ala1.000
alr3841662c.-242A>G0.326
embC4242550c.2688C>G1.000
embC4242643c.2781C>T1.000
ethA4326739c.735G>C1.000
ethR4328004c.456G>A1.000

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;