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: 5dc3aac95d608
Sample: 5dc3aac95d608

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Summary
ID: 5dc3aac95d608
Date: Thu Nov 7 05:27:11 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.37)
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

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB762879p.Met1025Leu0.132
rpoB762896c.3090G>C0.200
rpoB762925p.Thr1040Ile0.167
rpoB762938c.3132G>C0.115
rpoB762939p.Met1045Leu0.148
rpoB762942p.Ile1046Val0.151
rpoB762953c.3147G>A0.109
rpoB762965c.3159T>C0.130
rpoB763031c.3225T>C1.000
rpoC764641c.1272C>T0.109
rpoC764650c.1281G>T0.111
rpsL781395c.-165T>C1.000
embR1416870p.Glu160Lys0.161
rrs1472137r.292g>a0.333
rrs1472150r.305t>a0.452
rrs1472151r.306c>t0.452
rrs1472172r.327t>c0.574
rrs1472203r.358g>a0.197
rrs1472210r.365a>t0.179
rrs1472214r.369c>g0.404
rrs1472225r.380c>a0.193
rrs1472235r.390g>c0.357
rrs1472240r.395g>c0.352
rrs1472242r.397c>t0.365
rrs1472251r.406g>a0.163
rrs1472252r.407g>a0.137
rrs1472253r.408g>t0.137
rrs1472259r.414c>a0.280
rrs1472264r.419t>c0.146
rrs1472266r.421c>a0.146
rrs1472277r.432c>g0.143
rrs1472344r.499c>t0.231
rrs1472389r.544g>a0.243
rrs1472390r.545t>a0.243
rrs1472391r.546c>t0.243
rrs1472530r.685g>a0.192
rrs1472537r.692c>t0.192
rrs1472544r.699c>a0.208
rrs1472545r.700a>t0.192
rrs1472566r.721g>a0.276
rrs1472571r.726g>c0.276
rrs1472579r.734g>c0.241
rrs1472580r.735c>t0.226
rrs1472581r.736a>t0.267
rrs1472598r.753a>c0.375
rrs1472599r.754g>t0.340
rrs1472616r.771g>a0.474
rrs1472655r.810g>a0.270
rrs1472658r.813g>a0.270
rrs1472661r.816a>g0.286
rrs1472670r.825g>t0.200
rrs1472673r.828t>g0.229
rrs1472675r.830t>c0.211
rrs1472677r.832c>t0.189
rrs1472690r.845c>a0.243
rrs1472697r.852t>c0.386
rrs1472713r.868t>c0.481
rrs1472716r.871c>t0.526
rrs1472734r.889c>t0.162
rrs1472741r.896g>a0.174
rrs1472742r.897c>t0.632
rrs1472744r.899a>g0.486
rrs1472767r.922g>a0.118
rrs1472781r.936c>t0.667
rrs1472793r.948a>t0.644
rrs1472803r.958t>a0.509
rrs1472812r.967a>c0.164
rrs1472887r.1042g>c0.309
rrs1472895r.1050c>t0.311
rrs1473163r.1318c>t0.167
rrs1473164r.1319c>g0.118
rrs1473177r.1332g>a0.293
rrs1473192r.1347a>g0.266
rrs1473205r.1360t>c0.279
rrs1473352r.1507c>t0.306
rrl1474218r.561t>a0.277
rrl1474228r.571t>c0.277
rrl1474249r.592g>t0.304
rrl1474252r.595t>a0.289
rrl1475783r.2126t>g0.310
rrl1475791r.2134a>g0.164
rrl1475803r.2146t>c0.524
rrl1475804r.2147g>c0.524
rrl1475816r.2159c>g0.562
rrl1475817r.2160a>g0.562
rrl1475881r.2224t>c0.167
rrl1475883r.2226a>c0.161
rrl1475892r.2235a>c0.156
rrl1475894r.2237c>g0.152
rrl1475904r.2247g>a0.167
rrl1476332r.2675g>c0.181
rrl1476336r.2679c>t0.165
rrl1476338r.2681c>t0.224
rrl1476353r.2696g>t0.152
rrl1476358r.2701t>c0.289
rrl1476369r.2712c>t0.291
rrl1476372r.2715t>c0.163
rrl1476382r.2725a>g0.347
rrl1476383r.2726t>a0.290
rrl1476384r.2727g>t0.186
rrl1476408r.2751g>a0.226
rrl1476411r.2754g>t0.117
rrl1476425r.2768g>t0.343
rrl1476428r.2771c>t0.283
rrl1476429r.2772a>c0.352
rrl1476442r.2785t>a0.168
rrl1476443r.2786g>t0.222
rrl1476455r.2798c>a0.222
rrl1476456r.2799a>t0.159
rrl1476463r.2806c>t0.108
rrl1476466r.2809c>t0.221
rrl1476470r.2813c>t0.273
rrl1476474r.2817c>t0.111
rrl1476481r.2824t>c0.485
rrl1476506r.2849t>c0.491
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
embA4245818c.2586C>T1.000
ethA4326053p.Asp474Gly0.978
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;