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: 5dd3a75f7bb71
Sample: 5dd3a75f7bb71

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Summary
ID: 5dd3a75f7bb71
Date: Tue Nov 19 08:30:41 2019
Strain: lineage4.6.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRgid c.102 102del (1.00)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1401a>g (0.47)
CapreomycinRrrs r.1401a>g (0.47)
KanamycinRrrs r.1401a>g (0.47)

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
rpoB762888p.His1028Asn0.128
rpoB762896c.3090G>T0.174
rpoB762899c.3093G>C0.239
rpoB762917c.3111C>T0.182
rpoB762923c.3117C>G0.222
rpoB762925p.Thr1040Ile0.222
rpoB762929c.3123G>T0.179
rpoB762932c.3126G>T0.152
rpoB762939p.Met1045Leu0.286
rpoB762942p.Ile1046Val0.298
rpoB762965c.3159T>C0.293
rpoB762980c.3174T>C0.262
rpoB762983c.3177C>A0.175
rpoB762989c.3183G>C0.255
rpoB762998c.3192G>A0.280
rpoC764566c.1197C>G0.256
rpoC764575c.1206T>C0.289
rpoC764581c.1212T>C0.359
rpoC764582p.Leu405Met0.350
rpoC764605c.1236G>C0.388
rpoC764611c.1242G>C0.375
rpoC764620c.1251G>T0.320
rpoC764632c.1263T>C0.440
rpoC764641c.1272C>T0.380
rpoC764644c.1275G>C0.320
rpoC764650c.1281G>T0.396
rpoC764663p.Val432Thr0.156
rpoC764668c.1299C>T0.163
rpoC764672p.Gln435Glu0.195
rpoC764677c.1308C>G0.154
rpoC764695c.1326T>C0.262
rpoC764706p.Leu446Gln0.143
rpoC764716c.1347G>C0.150
rpoC764902c.1533C>T0.119
rpoC764908c.1539G>A0.136
rpoC764911c.1542A>C0.136
rpoC764920c.1551G>C0.182
rpoC764935c.1566T>C0.196
rpoC764944c.1575C>T0.163
rpoC764948c.1579T>C0.163
rpoC764953c.1584G>C0.220
rpoC764956c.1587T>C0.167
rpoC764957p.Glu530Thr0.167
rpoC764962c.1593G>C0.163
rpoC764968c.1599T>C0.286
rpsL781395c.-165T>C1.000
rpsL781670c.111G>T0.156
rrs1471876r.31g>a0.480
rrs1471892r.47g>a0.462
rrs1471893r.48t>g0.423
rrs1472106r.261g>a0.453
rrs1472108r.263c>a0.453
rrs1472160r.315c>t0.632
rrs1472172r.327t>c0.735
rrs1472181r.336g>a0.634
rrs1472214r.369c>g0.748
rrs1472235r.390g>c0.689
rrs1472240r.395g>c0.710
rrs1472242r.397c>t0.708
rrs1472251r.406g>a0.610
rrs1472253r.408g>t0.566
rrs1472259r.414c>a0.627
rrs1472266r.421c>a0.529
rrs1472277r.432c>g0.450
rrs1472338r.493a>c0.637
rrs1472344r.499c>t0.686
rrs1472349r.504a>t0.665
rrs1472374r.529t>a0.686
rrs1472379r.534t>g0.656
rrs1472382r.537g>t0.703
rrs1472391r.546c>t0.717
rrs1472412r.567a>c0.367
rrs1472415r.570t>a0.296
rrs1472557r.712g>a0.367
rrs1472598r.753a>t0.770
rrs1472616r.771g>a0.762
rrs1472697r.852t>c0.149
rrs1472712r.867g>a0.303
rrs1472713r.868t>c0.306
rrs1472715r.870c>t0.333
rrs1472716r.871c>t0.394
rrs1472734r.889c>t0.601
rrs1472741r.896g>a0.592
rrs1472742r.897c>t0.655
rrs1472781r.936c>t0.684
rrs1472793r.948a>t0.642
rrs1472803r.958t>a0.590
rrs1472812r.967a>c0.544
rrs1472887r.1042g>c0.665
rrs1473038r.1193a>c0.602
rrs1473044r.1199c>g0.649
rrs1473051r.1206t>c0.127
rrs1473053r.1208t>g0.132
rrs1473056r.1211a>t0.130
rrs1473062r.1217t>a0.144
rrs1473068r.1223a>g0.132
rrs1473173r.1328c>t0.323
rrs1473177r.1332g>a0.440
rrs1473199r.1354ca>c0.509
rrs1473202r.1357c>t0.449
rrs1473352r.1507c>g0.363
rrs1473353r.1508c>g0.357
rrs1473358r.1513g>c0.349
rrs1473359r.1514g>c0.349
rrl1473922r.265a>c0.371
rrl1474199r.542g>a0.427
rrl1474201r.544t>c0.422
rrl1474202r.545t>a0.420
rrl1474218r.561t>a0.530
rrl1474228r.571t>c0.452
rrl1474235r.578g>c0.379
rrl1474249r.592g>t0.383
rrl1474252r.595t>a0.361
rrl1474264r.607t>g0.346
rrl1474265r.608g>a0.341
rrl1474558r.901g>c0.509
rrl1474584r.927c>g0.511
rrl1474586r.929t>a0.503
rrl1474587r.930g>a0.497
rrl1474602r.945c>g0.480
rrl1474828r.1171g>c0.406
rrl1474844r.1187g>t0.475
rrl1474864r.1207c>t0.408
rrl1474866r.1209c>a0.403
rrl1474869r.1212g>t0.406
rrl1474875r.1218g>a0.412
rrl1474876r.1219t>a0.406
rrl1474883r.1226t>c0.417
rrl1475499r.1842c>g0.411
rrl1475526r.1869c>t0.506
rrl1475538r.1881t>c0.421
rrl1475539r.1882a>t0.407
rrl1475540r.1883c>t0.401
rrl1475545r.1888t>g0.407
rrl1475553r.1896g>t0.365
rrl1475555r.1898t>g0.369
rrl1475571r.1914a>t0.377
rrl1475575r.1918c>a0.365
rrl1475577r.1920c>g0.354
rrl1475589r.1932g>a0.370
rrl1475672r.2015c>t0.286
rrl1475673r.2016t>c0.284
rrl1475685r.2028t>g0.325
rrl1475687r.2030c>t0.325
rrl1475688r.2031g>c0.323
rrl1475697r.2040c>a0.400
rrl1475702r.2045g>t0.397
rrl1475707r.2050t>c0.394
rrl1475713r.2056c>g0.388
rrl1475716r.2059a>t0.380
rrl1475803r.2146t>c0.395
rrl1475804r.2147g>c0.406
rrl1475816r.2159c>g0.399
rrl1475817r.2160a>g0.408
rrl1476141r.2484a>g0.265
rrl1476153r.2496t>c0.261
rrl1476160r.2503t>g0.222
rrl1476164r.2507a>g0.269
rrl1476165r.2508t>a0.270
rrl1476252r.2595t>g0.376
rrl1476260r.2603a>g0.372
rrl1476266r.2609g>a0.375
rrl1476279r.2622g>t0.189
rrl1476280r.2623a>c0.188
rrl1476281r.2624t>a0.190
rrl1476293r.2636c>t0.195
rrl1476294r.2637a>g0.196
rrl1476295r.2638c>g0.201
rrl1476296r.2639c>t0.203
rrl1476301r.2644a>t0.219
rrl1476311r.2654g>c0.214
rrl1476312r.2655t>c0.209
rrl1476313r.2656g>a0.217
rrl1476336r.2679c>g0.594
rrl1476356r.2699c>g0.591
rrl1476357r.2700t>a0.593
rrl1476358r.2701t>c0.586
rrl1476382r.2725a>g0.649
rrl1476384r.2727g>t0.677
rrl1476404r.2747g>a0.622
rrl1476408r.2751g>a0.697
rrl1476442r.2785t>a0.561
rrl1476443r.2786g>t0.622
rrl1476455r.2798c>a0.642
rrl1476456r.2799a>t0.595
rrl1476466r.2809c>t0.643
rrl1476470r.2813c>t0.606
rrl1476474r.2817c>t0.552
rrl1476481r.2824t>c0.568
rrl1476506r.2849t>c0.517
rrl1476567r.2910c>t0.494
rrl1476573r.2916a>t0.488
rrl1476575r.2918c>t0.488
rrl1476584r.2927c>g0.325
rrl1476586r.2929c>t0.270
rrl1476588r.2931a>t0.270
rrl1476596r.2939c>t0.217
rrl1476601r.2944g>a0.210
rrl1476645r.2988a>g0.399
tlyA1917972c.33A>G1.000
thyX3067474p.Pro158Ala1.000
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;