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.
Back to results page.
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: 5da927d0d3882
Sample: 5da927d0d3882

Download results

Summary
ID: 5da927d0d3882
Date: Fri Oct 18 03:50:00 2019
Strain: lineage4.6.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
RifampicinRrpoB p.Ser450Leu (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
rpoB759940p.Pro45Leu1.000
rpoC764353c.984G>T0.151
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.379
rrs1471900r.55c>t0.379
rrs1472106r.261g>a0.143
rrs1472113r.268t>c0.133
rrs1472127r.282c>t0.313
rrs1472129r.284g>c0.337
rrs1472137r.292g>a0.352
rrs1472150r.305t>a0.381
rrs1472151r.306c>a0.381
rrs1472172r.327t>c0.443
rrs1472203r.358g>a0.396
rrs1472210r.365a>c0.394
rrs1472213r.368g>c0.379
rrs1472225r.380c>a0.377
rrs1472236r.391c>g0.377
rrs1472240r.395g>a0.375
rrs1472251r.406g>a0.345
rrs1472253r.408g>t0.333
rrs1472256r.411t>g0.315
rrs1472259r.414c>a0.333
rrs1472271r.426t>c0.301
rrs1472344r.499c>t0.525
rrs1472379r.534t>g0.581
rrs1472400r.555c>t0.523
rrs1472530r.685g>a0.301
rrs1472537r.692c>t0.284
rrs1472541r.696t>g0.268
rrs1472544r.699c>g0.277
rrs1472545r.700a>t0.277
rrs1472557r.712g>a0.403
rrs1472571r.726g>c0.389
rrs1472573r.728c>t0.378
rrs1472579r.734g>a0.378
rrs1472581r.736a>t0.378
rrs1472598r.753a>c0.435
rrs1472616r.771g>a0.476
rrs1472700r.855c>t0.143
rrs1472705r.860g>a0.190
rrs1472713r.868t>c0.421
rrs1472716r.871c>t0.446
rrs1472734r.889c>t0.466
rrs1472741r.896g>a0.457
rrs1472744r.899a>g0.451
rrs1472767r.922g>a0.462
rrs1472779r.934g>a0.441
rrs1472781r.936c>t0.451
rrs1472786r.941c>t0.425
rrs1472793r.948a>t0.453
rrs1472803r.958t>a0.470
rrs1472895r.1050c>t0.490
rrs1472987r.1142g>t0.131
rrs1472988r.1143t>a0.128
rrs1473020r.1175t>c0.331
rrs1473035r.1190g>a0.336
rrs1473053r.1208t>a0.234
rrs1473056r.1211a>t0.241
rrs1473062r.1217t>a0.245
rrs1473068r.1223a>g0.228
rrs1473070r.1225g>a0.228
rrs1473145r.1300c>t0.236
rrs1473147r.1302g>c0.225
rrs1473148r.1303g>a0.218
rrs1473150r.1305t>g0.217
rrs1473161r.1316a>c0.204
rrs1473163r.1318c>t0.213
rrs1473164r.1319c>g0.213
rrs1473166r.1321g>a0.205
rrs1473177r.1332g>a0.282
rrs1473179r.1334c>t0.264
rrs1473192r.1347a>g0.323
rrs1473202r.1357c>t0.286
rrs1473205r.1360t>c0.274
rrs1473226r.1381c>t0.360
rrs1473352r.1507c>t0.322
rrl1474218r.561t>a0.231
rrl1474330r.673a>t0.275
rrl1474387r.730c>a0.161
rrl1474406r.749t>c0.174
rrl1474565r.908t>a0.317
rrl1474570r.913g>t0.315
rrl1474571r.914g>t0.311
rrl1474578r.921a>g0.322
rrl1474584r.927c>g0.337
rrl1474586r.929t>a0.337
rrl1474768r.1111c>g0.224
rrl1474779r.1122g>a0.252
rrl1474780r.1123c>t0.257
rrl1474782r.1125g>a0.264
rrl1474790r.1133c>t0.305
rrl1474798r.1141c>t0.392
rrl1474804r.1147c>t0.422
rrl1474823r.1166c>g0.469
rrl1474827r.1170c>t0.466
rrl1474830r.1173a>g0.475
rrl1474844r.1187g>t0.530
rrl1474866r.1209c>a0.570
rrl1474869r.1212g>t0.554
rrl1474896r.1239a>g0.485
rrl1474902r.1245t>c0.463
rrl1474904r.1247g>c0.466
rrl1474913r.1256t>a0.425
rrl1474920r.1263g>a0.374
rrl1475122r.1465c>t0.271
rrl1475129r.1472g>a0.278
rrl1475154r.1497c>a0.280
rrl1475167r.1510t>a0.289
rrl1475175r.1518g>a0.265
rrl1475182r.1525t>a0.262
rrl1475188r.1531c>t0.242
rrl1475498r.1841c>g0.180
rrl1475574r.1917c>a0.327
rrl1475672r.2015c>g0.228
rrl1475673r.2016t>c0.224
rrl1475687r.2030c>t0.271
rrl1475696r.2039t>c0.285
rrl1475703r.2046a>g0.285
rrl1475707r.2050t>a0.295
rrl1475716r.2059a>g0.290
rrl1475803r.2146t>c0.359
rrl1475804r.2147g>c0.359
rrl1475816r.2159c>g0.340
rrl1475817r.2160a>g0.350
rrl1475843r.2186g>a0.312
rrl1475849r.2192g>a0.325
rrl1475853r.2196c>t0.316
rrl1475858r.2201t>c0.327
rrl1476153r.2496t>c0.173
rrl1476181r.2524a>c0.174
rrl1476251r.2594t>c0.333
rrl1476260r.2603a>g0.408
rrl1476280r.2623a>c0.376
rrl1476293r.2636c>t0.205
rrl1476294r.2637a>g0.198
rrl1476295r.2638c>g0.200
rrl1476296r.2639c>t0.200
rrl1476297r.2640c>a0.200
rrl1476302r.2645g>a0.198
rrl1476311r.2654g>c0.173
rrl1476312r.2655t>c0.175
rrl1476313r.2656g>a0.176
rrl1476332r.2675g>c0.396
rrl1476338r.2681c>t0.408
rrl1476353r.2696g>t0.414
rrl1476358r.2701t>c0.431
rrl1476372r.2715t>c0.466
rrl1476382r.2725a>g0.440
rrl1476383r.2726t>a0.442
rrl1476408r.2751g>a0.483
rrl1476425r.2768g>a0.474
rrl1476428r.2771c>t0.487
rrl1476466r.2809c>t0.536
rrl1476481r.2824t>c0.485
rrl1476506r.2849t>c0.458
rrl1476547r.2890c>t0.307
rrl1476567r.2910c>t0.348
rrl1476573r.2916a>c0.364
rrl1476577r.2920t>g0.370
rrl1476584r.2927c>t0.354
rrl1476594r.2937c>t0.229
rrl1476595r.2938c>t0.208
rrl1476603r.2946g>a0.205
rrl1476607r.2950c>t0.176
rrl1476608r.2951c>a0.179
rrl1476614r.2957a>g0.200
rrl1476621r.2964c>a0.185
rrl1476624r.2967t>g0.179
rrl1476628r.2971t>a0.174
rrl1476629r.2972c>a0.176
rrl1476630r.2973a>g0.176
rrl1476637r.2980c>g0.410
tlyA1917972c.33A>G1.000
thyX3067474p.Pro158Ala1.000
alr3841654c.-234A>C0.191
alr3841662c.-242A>G1.000
alr3841663c.-243G>A0.244
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;