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: 5dd217cfd629a
Sample: 5dd217cfd629a

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Summary
ID: 5dd217cfd629a
Date: Mon Nov 18 04:05:58 2019
Strain: lineage1.2.1
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239
lineage1.2.1Indo-OceanicEAI2RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6112p.Met291Ile1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8452p.Ala384Val1.000
gyrA9143c.1842T>C1.000
gyrA9260c.1959G>C1.000
gyrA9304p.Gly668Asp1.000
rpoB760928c.1122G>T1.000
rpoB763031c.3225T>C1.000
rpoC763531c.162G>C1.000
rpoC763884p.Ala172Val1.000
rpoC763886c.517C>A1.000
rpsL781395c.-165T>C1.000
rplC801435c.627C>T1.000
embR1417019p.Cys110Tyr1.000
embR1417554c.-207C>G1.000
rrs1471896r.51t>c0.336
rrs1471900r.55c>t0.286
rrs1472127r.282c>t0.270
rrs1472129r.284g>c0.278
rrs1472137r.292g>a0.288
rrs1472150r.305t>a0.281
rrs1472151r.306c>t0.281
rrs1472172r.327t>c0.365
rrs1472203r.358g>a0.349
rrs1472378r.533g>t0.293
rrs1472379r.534t>g0.345
rrs1472382r.537g>a0.309
rrs1472400r.555c>t0.345
rrs1472530r.685g>a0.152
rrs1472537r.692c>t0.159
rrs1472541r.696t>g0.156
rrs1472544r.699c>g0.156
rrs1472545r.700a>t0.182
rrs1472557r.712g>a0.256
rrs1472570r.725g>a0.308
rrs1472571r.726g>c0.300
rrs1472579r.734g>t0.321
rrs1472581r.736a>t0.321
rrs1472598r.753a>c0.371
rrs1472713r.868t>c0.217
rrs1472716r.871c>t0.227
rrs1472734r.889c>t0.271
rrs1472741r.896g>a0.283
rrs1472744r.899a>g0.271
rrs1472781r.936c>t0.393
rrs1472793r.948a>t0.409
rrs1472803r.958t>a0.424
rrs1472895r.1050c>t0.342
rrs1473035r.1190g>a0.348
rrs1473053r.1208t>a0.364
rrs1473056r.1211a>t0.364
rrs1473062r.1217t>a0.376
rrs1473068r.1223a>g0.378
rrs1473080r.1235c>g0.351
rrs1473082r.1237g>a0.361
rrs1473084r.1239t>a0.366
rrs1473094r.1249t>a0.333
rrs1473099r.1254t>a0.268
rrs1473109r.1264t>c0.200
rrs1473115r.1270g>c0.179
rrs1473147r.1302g>c0.364
rrs1473148r.1303g>a0.362
rrs1473163r.1318c>t0.336
rrs1473164r.1319c>g0.339
rrs1473172r.1327t>c0.339
rrs1473173r.1328c>t0.349
rrs1473177r.1332g>a0.378
rrs1473192r.1347a>g0.473
rrs1473202r.1357c>t0.422
rrs1473205r.1360t>c0.414
rrs1473352r.1507c>t0.421
rrl1473679r.22t>c0.155
rrl1473851r.194g>c0.226
rrl1473862r.205c>a0.222
rrl1473871r.214t>g0.240
rrl1473876r.219g>a0.250
rrl1474218r.561t>a0.300
rrl1474228r.571t>c0.267
rrl1474236r.579g>a0.250
rrl1474252r.595t>a0.293
rrl1474253r.596a>t0.293
rrl1474552r.895c>g0.212
rrl1474570r.913g>t0.219
rrl1474584r.927c>g0.200
rrl1474586r.929t>a0.222
rrl1474639r.982g>a1.000
rrl1474747r.1090c>a0.453
rrl1474753r.1096ac>a0.462
rrl1474777r.1120t>c0.471
rrl1474782r.1125g>a0.489
rrl1474790r.1133c>t0.233
rrl1474794r.1137c>a0.206
rrl1474812r.1155g>a0.256
rrl1474823r.1166c>g0.333
rrl1474827r.1170c>t0.333
rrl1474830r.1173a>t0.295
rrl1474831r.1174a>t0.295
rrl1474844r.1187g>t0.354
rrl1474866r.1209c>a0.405
rrl1474869r.1212g>t0.405
rrl1474896r.1239a>g0.395
rrl1474902r.1245t>c0.381
rrl1474904r.1247g>c0.390
rrl1474913r.1256t>a0.375
rrl1474920r.1263g>c0.375
rrl1475122r.1465c>t0.174
rrl1475129r.1472g>t0.200
rrl1475144r.1487g>c0.207
rrl1475154r.1497c>a0.206
rrl1475163r.1506t>g0.161
rrl1475574r.1917c>a0.434
rrl1475713r.2056c>g0.161
rrl1475716r.2059a>g0.164
rrl1475783r.2126t>g0.321
rrl1475803r.2146t>c0.419
rrl1475804r.2147g>c0.419
rrl1475816r.2159c>g0.444
rrl1475817r.2160a>g0.459
rrl1475858r.2201t>c0.391
rrl1475866r.2209t>a0.339
rrl1475871r.2214t>c0.300
rrl1476141r.2484a>g0.233
rrl1476153r.2496t>c0.246
rrl1476165r.2508t>g0.210
rrl1476225r.2568t>g0.354
rrl1476251r.2594t>c0.436
rrl1476260r.2603a>g0.433
rrl1476280r.2623a>c0.446
rrl1476293r.2636c>t0.213
rrl1476294r.2637a>g0.213
rrl1476295r.2638c>g0.210
rrl1476296r.2639c>t0.226
rrl1476297r.2640c>t0.194
rrl1476301r.2644a>c0.188
rrl1476302r.2645g>a0.185
rrl1476311r.2654g>c0.191
rrl1476312r.2655t>c0.191
rrl1476313r.2656g>a0.194
rrl1476332r.2675g>c0.322
rrl1476353r.2696g>t0.318
rrl1476358r.2701t>c0.305
rrl1476372r.2715t>c0.314
rrl1476382r.2725a>g0.313
rrl1476383r.2726t>a0.321
rrl1476408r.2751g>a0.357
rrl1476425r.2768g>t0.296
rrl1476428r.2771c>t0.299
rrl1476429r.2772a>c0.309
rrl1476458r.2801t>c0.656
rrl1476466r.2809c>t0.384
rrl1476481r.2824t>c0.344
rrl1476506r.2849t>c0.270
rrl1476547r.2890c>t0.144
rrl1476567r.2910c>t0.165
rrl1476577r.2920t>g0.162
rrl1476584r.2927c>t0.169
fabG11674162c.723C>T1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518132c.18C>T1.000
kasA2519048p.Gly312Ser1.000
ald3086788c.-32T>C1.000
fbiA3640557c.15T>C1.000
alr3841662c.-242A>G0.224
embC4240671p.Thr270Ile1.000
embC4241042p.Asn394Asp1.000
embC4242643c.2781C>T1.000
embA4243580c.348G>A1.000
embA4244420c.1188G>C1.000
embA4245969p.Pro913Ser1.000
embB4246584p.Arg24Pro0.500
embB4247578c.1065G>A1.000
embB4247646p.Glu378Ala1.000
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;