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: 5dcb85116f8e8
Sample: 5dcb85116f8e8

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Summary
ID: 5dcb85116f8e8
Date: Wed Nov 13 04:25:28 2019
Strain: lineage2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.His445Tyr (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8650p.Arg450His1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpoC765121c.1752G>A1.000
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.339
rrs1471900r.55c>t0.339
rrs1472106r.261g>a0.139
rrs1472112r.267c>t0.141
rrs1472113r.268t>c0.139
rrs1472127r.282c>t0.210
rrs1472129r.284g>c0.207
rrs1472137r.292g>a0.220
rrs1472150r.305t>a0.260
rrs1472151r.306c>a0.263
rrs1472172r.327t>c0.356
rrs1472203r.358g>a0.434
rrs1472210r.365a>c0.386
rrs1472213r.368g>c0.403
rrs1472215r.370a>g0.403
rrs1472225r.380c>a0.393
rrs1472234r.389t>c0.386
rrs1472236r.391c>g0.379
rrs1472240r.395g>a0.373
rrs1472344r.499c>t0.353
rrs1472379r.534t>g0.348
rrs1472382r.537g>a0.348
rrs1472400r.555c>t0.351
rrs1472507r.662c>g0.234
rrs1472517r.672t>a0.304
rrs1472518r.673g>c0.283
rrs1472530r.685g>a0.375
rrs1472537r.692c>t0.379
rrs1472544r.699c>g0.400
rrs1472545r.700a>t0.400
rrs1472557r.712g>a0.393
rrs1472570r.725g>a0.386
rrs1472571r.726g>c0.386
rrs1472581r.736a>t0.382
rrs1472598r.753a>c0.410
rrs1472616r.771g>a0.352
rrs1472734r.889c>t0.391
rrs1472741r.896g>a0.370
rrs1472744r.899a>g0.382
rrs1472767r.922g>a0.395
rrs1472779r.934g>a0.371
rrs1472781r.936c>t0.382
rrs1472786r.941c>t0.394
rrs1472793r.948a>t0.391
rrs1472803r.958t>a0.418
rrs1472895r.1050c>t0.545
rrs1473020r.1175t>c0.389
rrs1473035r.1190g>a0.378
rrs1473056r.1211a>t0.211
rrs1473062r.1217t>a0.214
rrs1473070r.1225g>a0.211
rrs1473081r.1236c>t0.243
rrs1473089r.1244a>c0.172
rrs1473093r.1248c>a0.164
rrs1473094r.1249t>a0.159
rrs1473099r.1254t>a0.159
rrs1473177r.1332g>a0.258
rrs1473179r.1334c>t0.270
rrs1473192r.1347a>g0.299
rrs1473202r.1357c>t0.221
rrs1473205r.1360t>c0.224
rrs1473226r.1381c>t0.317
rrs1473352r.1507c>t0.396
rrl1474218r.561t>a0.271
rrl1474228r.571t>c0.236
rrl1474236r.579g>a0.200
rrl1474249r.592g>t0.184
rrl1474252r.595t>a0.163
rrl1474269r.612c>t0.128
rrl1474330r.673a>t0.140
rrl1474527r.870t>g0.154
rrl1474530r.873g>t0.154
rrl1474539r.882c>a0.171
rrl1474542r.885a>c0.182
rrl1474552r.895c>g0.189
rrl1474555r.898t>g0.200
rrl1474562r.905g>c0.194
rrl1474565r.908t>a0.206
rrl1474570r.913g>t0.211
rrl1474571r.914g>t0.190
rrl1474578r.921a>g0.234
rrl1474584r.927c>g0.231
rrl1474586r.929t>a0.231
rrl1474777r.1120t>c0.200
rrl1474779r.1122g>a0.205
rrl1474780r.1123c>t0.211
rrl1474782r.1125g>a0.200
rrl1474790r.1133c>t0.238
rrl1474798r.1141c>t0.340
rrl1474804r.1147c>t0.362
rrl1474823r.1166c>g0.412
rrl1474827r.1170c>t0.420
rrl1474831r.1174a>c0.438
rrl1474844r.1187g>t0.453
rrl1474866r.1209c>a0.420
rrl1474869r.1212g>t0.396
rrl1474896r.1239a>g0.345
rrl1474902r.1245t>c0.345
rrl1474904r.1247g>c0.352
rrl1474913r.1256t>a0.291
rrl1474920r.1263g>a0.260
rrl1475574r.1917c>a0.273
rrl1475672r.2015c>g0.204
rrl1475673r.2016t>c0.204
rrl1475687r.2030c>t0.259
rrl1475696r.2039t>c0.212
rrl1475699r.2042c>t0.204
rrl1475703r.2046a>g0.196
rrl1475707r.2050t>a0.218
rrl1475716r.2059a>g0.228
rrl1475803r.2146t>c0.291
rrl1475804r.2147g>c0.291
rrl1475816r.2159c>g0.309
rrl1475817r.2160a>g0.315
rrl1475843r.2186g>a0.288
rrl1475849r.2192g>a0.302
rrl1475853r.2196c>t0.309
rrl1475858r.2201t>c0.339
rrl1476126r.2469c>t0.192
rrl1476128r.2471t>a0.189
rrl1476135r.2478t>c0.175
rrl1476141r.2484a>g0.159
rrl1476153r.2496t>c0.164
rrl1476164r.2507a>g0.155
rrl1476165r.2508t>a0.153
rrl1476181r.2524a>c0.151
rrl1476251r.2594t>c0.275
rrl1476260r.2603a>g0.289
rrl1476280r.2623a>c0.226
rrl1476332r.2675g>c0.267
rrl1476338r.2681c>t0.290
rrl1476353r.2696g>t0.274
rrl1476358r.2701t>c0.271
rrl1476372r.2715t>c0.354
rrl1476382r.2725a>g0.346
rrl1476383r.2726t>a0.360
rrl1476408r.2751g>a0.443
rrl1476425r.2768g>a0.459
rrl1476428r.2771c>t0.486
rrl1476466r.2809c>t0.406
rrl1476481r.2824t>c0.429
rrl1476506r.2849t>c0.323
rrl1476547r.2890c>t0.123
rrl1476567r.2910c>t0.218
rrl1476573r.2916a>t0.227
rrl1476577r.2920t>g0.233
rrl1476594r.2937c>t0.239
rrl1476637r.2980c>g0.202
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ahpC2726468c.276G>A1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.360
alr3841654c.-234A>C0.379
embC4242643c.2781C>T1.000
embA4246088c.2856A>G1.000
embB4246584p.Arg24Pro0.423
embB4248564p.Ala684Val1.000
ethR4327641c.93C>G1.000
gid4407588c.615T>C1.000

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;