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: 5dca2dda3d69f
Sample: 5dca2dda3d69f

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Summary
ID: 5dca2dda3d69f
Date: Tue Nov 12 04:01:32 2019
Strain: lineage1.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
RifampicinRrpoB p.Ser450Leu (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1401a>g (0.58)
CapreomycinRrrs r.1401a>g (0.58)
KanamycinRrrs r.1401a>g (0.58)

Lineage2FamilyMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6112p.Met291Ile1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8452p.Ala384Val1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
rpoB761770p.Met655Thr1.000
rpoB763031c.3225T>C1.000
rpoC763884p.Ala172Val1.000
rpoC763886c.517C>A1.000
rpoC765171p.Pro601Leu1.000
rpsL781395c.-165T>C1.000
embR1417019p.Cys110Tyr1.000
embR1417554c.-207C>G1.000
rrs1471896r.51t>c0.479
rrs1471900r.55c>t0.466
rrs1472106r.261g>a0.243
rrs1472112r.267c>t0.247
rrs1472113r.268t>c0.267
rrs1472127r.282c>t0.418
rrs1472129r.284g>c0.444
rrs1472137r.292g>a0.418
rrs1472150r.305t>a0.433
rrs1472151r.306c>a0.439
rrs1472172r.327t>c0.465
rrs1472203r.358g>a0.495
rrs1472210r.365a>c0.461
rrs1472213r.368g>c0.448
rrs1472215r.370a>g0.448
rrs1472225r.380c>a0.414
rrs1472234r.389t>c0.354
rrs1472236r.391c>g0.349
rrs1472240r.395g>a0.322
rrs1472344r.499c>t0.360
rrs1472379r.534t>g0.341
rrs1472382r.537g>a0.346
rrs1472400r.555c>t0.354
rrs1472507r.662c>g0.183
rrs1472517r.672t>a0.194
rrs1472518r.673g>c0.197
rrs1472530r.685g>a0.333
rrs1472537r.692c>t0.357
rrs1472544r.699c>g0.373
rrs1472545r.700a>t0.373
rrs1472557r.712g>a0.384
rrs1472570r.725g>a0.381
rrs1472571r.726g>c0.381
rrs1472581r.736a>t0.451
rrs1472598r.753a>c0.470
rrs1472616r.771g>a0.480
rrs1472734r.889c>t0.500
rrs1472741r.896g>a0.492
rrs1472744r.899a>g0.468
rrs1472767r.922g>a0.442
rrs1472779r.934g>a0.438
rrs1472781r.936c>t0.436
rrs1472786r.941c>t0.451
rrs1472793r.948a>t0.470
rrs1472803r.958t>a0.458
rrs1472895r.1050c>t0.587
rrs1473020r.1175t>c0.435
rrs1473035r.1190g>a0.426
rrs1473053r.1208t>a0.288
rrs1473055r.1210c>t0.283
rrs1473056r.1211a>t0.283
rrs1473062r.1217t>a0.306
rrs1473068r.1223a>g0.300
rrs1473070r.1225g>a0.306
rrs1473081r.1236c>t0.390
rrs1473089r.1244a>c0.286
rrs1473093r.1248c>a0.271
rrs1473094r.1249t>a0.262
rrs1473099r.1254t>a0.242
rrs1473110r.1265t>g0.137
rrs1473111r.1266a>g0.137
rrs1473115r.1270g>c0.149
rrs1473130r.1285g>a0.203
rrs1473177r.1332g>a0.413
rrs1473179r.1334c>t0.421
rrs1473192r.1347a>g0.444
rrs1473202r.1357c>t0.355
rrs1473205r.1360t>c0.351
rrs1473226r.1381c>t0.524
rrs1473352r.1507c>t0.569
rrl1473926r.269g>c0.172
rrl1474218r.561t>a0.328
rrl1474228r.571t>c0.282
rrl1474236r.579g>a0.268
rrl1474249r.592g>t0.192
rrl1474252r.595t>a0.194
rrl1474269r.612c>t0.129
rrl1474552r.895c>g0.143
rrl1474555r.898t>g0.145
rrl1474562r.905g>c0.145
rrl1474565r.908t>a0.167
rrl1474570r.913g>t0.153
rrl1474571r.914g>t0.155
rrl1474578r.921a>g0.156
rrl1474584r.927c>g0.167
rrl1474586r.929t>a0.154
rrl1474709r.1052g>t1.000
rrl1474777r.1120t>c0.204
rrl1474779r.1122g>a0.208
rrl1474780r.1123c>t0.213
rrl1474782r.1125g>a0.213
rrl1474790r.1133c>t0.231
rrl1474798r.1141c>t0.286
rrl1474804r.1147c>t0.305
rrl1474823r.1166c>g0.311
rrl1474827r.1170c>t0.328
rrl1474831r.1174a>c0.328
rrl1474844r.1187g>t0.300
rrl1474866r.1209c>a0.338
rrl1474869r.1212g>t0.333
rrl1474896r.1239a>g0.271
rrl1474902r.1245t>c0.271
rrl1474904r.1247g>c0.265
rrl1474913r.1256t>a0.234
rrl1474920r.1263g>a0.200
rrl1475574r.1917c>a0.314
rrl1475672r.2015c>g0.436
rrl1475673r.2016t>c0.436
rrl1475687r.2030c>t0.441
rrl1475696r.2039t>c0.431
rrl1475699r.2042c>t0.438
rrl1475703r.2046a>g0.431
rrl1475707r.2050t>a0.453
rrl1475716r.2059a>g0.467
rrl1475803r.2146t>c0.297
rrl1475804r.2147g>c0.297
rrl1475816r.2159c>g0.333
rrl1475817r.2160a>g0.333
rrl1475843r.2186g>a0.347
rrl1475849r.2192g>a0.386
rrl1475853r.2196c>t0.338
rrl1475858r.2201t>c0.362
rrl1476126r.2469c>t0.286
rrl1476128r.2471t>a0.291
rrl1476135r.2478t>c0.290
rrl1476141r.2484a>g0.277
rrl1476153r.2496t>c0.328
rrl1476164r.2507a>g0.304
rrl1476165r.2508t>a0.298
rrl1476181r.2524a>c0.235
rrl1476251r.2594t>c0.505
rrl1476260r.2603a>g0.500
rrl1476280r.2623a>c0.460
rrl1476293r.2636c>t0.222
rrl1476294r.2637a>g0.229
rrl1476295r.2638c>g0.243
rrl1476296r.2639c>t0.229
rrl1476297r.2640c>a0.229
rrl1476301r.2644a>c0.242
rrl1476302r.2645g>a0.239
rrl1476311r.2654g>c0.235
rrl1476312r.2655t>c0.235
rrl1476313r.2656g>a0.246
rrl1476332r.2675g>c0.538
rrl1476338r.2681c>t0.544
rrl1476353r.2696g>t0.548
rrl1476358r.2701t>c0.557
rrl1476372r.2715t>c0.476
rrl1476382r.2725a>g0.505
rrl1476383r.2726t>a0.514
rrl1476408r.2751g>a0.536
rrl1476425r.2768g>a0.525
rrl1476428r.2771c>t0.500
rrl1476466r.2809c>t0.472
rrl1476481r.2824t>c0.444
rrl1476506r.2849t>c0.389
rrl1476547r.2890c>t0.330
rrl1476567r.2910c>t0.385
rrl1476573r.2916a>t0.413
rrl1476577r.2920t>g0.425
rrl1476594r.2937c>t0.402
rrl1476603r.2946g>a0.264
rrl1476607r.2950c>t0.267
rrl1476608r.2951c>g0.264
rrl1476614r.2957a>g0.258
rrl1476619r.2962c>t0.267
rrl1476624r.2967t>a0.280
rrl1476628r.2971t>a0.287
rrl1476629r.2972c>a0.287
rrl1476630r.2973a>g0.296
rrl1476637r.2980c>g0.410
fabG11674048c.609G>A1.000
rpsA1834319p.Val260Ile1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518123c.9G>A1.000
kasA2518132c.18C>T1.000
ald3086788c.-32T>C1.000
embC4240671p.Thr270Ile1.000
embC4241042p.Asn394Asp1.000
embC4242643c.2781C>T1.000
embA4243848p.Val206Met1.000
embA4244096c.864C>T1.000
embA4245969p.Pro913Ser1.000
embB4246584p.Arg24Pro0.400
embB4247646p.Glu378Ala1.000
ethA4327075c.399G>A1.000
gid4407588c.615T>C1.000
gid4407873c.330C>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;