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: 5d856e4a83513
Sample: 5d856e4a83513

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Summary
ID: 5d856e4a83513
Date: Sat Sep 21 01:28:34 2019
Strain: lineage4.9
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.35)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.9Euro-American (H37Rv-like)T1None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
rpsL781395c.-165T>C1.000
rrs1472137r.292g>a0.219
rrs1472150r.305t>a0.219
rrs1472151r.306c>t0.221
rrs1472164r.319g>a0.220
rrs1472172r.327t>c0.210
rrs1472177r.332c>t0.220
rrs1472203r.358g>a0.250
rrs1472210r.365a>c0.230
rrs1472213r.368g>c0.235
rrs1472215r.370a>g0.240
rrs1472225r.380c>a0.256
rrs1472234r.389t>c0.241
rrs1472236r.391c>g0.239
rrs1472240r.395g>a0.239
rrs1472378r.533g>t0.182
rrs1472379r.534t>g0.188
rrs1472382r.537g>a0.193
rrs1472389r.544g>a0.205
rrs1472400r.555c>t0.195
rrs1472412r.567a>c0.200
rrs1472415r.570t>g0.203
rrs1472422r.577t>c0.198
rrs1472517r.672t>a0.183
rrs1472518r.673g>t0.183
rrs1472530r.685g>a0.181
rrs1472541r.696t>g0.173
rrs1472544r.699c>a0.175
rrs1472545r.700a>t0.175
rrs1472557r.712g>a0.226
rrs1472570r.725g>a0.232
rrs1472571r.726g>c0.232
rrs1472573r.728c>t0.232
rrs1472579r.734g>t0.241
rrs1472581r.736a>t0.247
rrs1472596r.751g>t0.271
rrs1472598r.753a>t0.264
rrs1472614r.769g>t0.250
rrs1472616r.771g>a0.253
rrs1472655r.810g>a0.161
rrs1472658r.813g>a0.143
rrs1472661r.816a>g0.143
rrs1472665r.820g>a0.143
rrs1472678r.833t>c0.140
rrs1472679r.834t>c0.138
rrs1472690r.845c>a0.143
rrs1472695r.850c>t0.159
rrs1472697r.852t>c0.157
rrs1472713r.868t>c0.296
rrs1472716r.871c>t0.311
rrs1472742r.897c>t0.339
rrs1472744r.899a>g0.336
rrs1472767r.922g>a0.342
rrs1472781r.936c>t0.361
rrs1472793r.948a>t0.346
rrs1472803r.958t>a0.333
rrs1472895r.1050c>t0.198
rrs1473145r.1300c>t0.135
rrs1473147r.1302g>t0.134
rrs1473148r.1303g>a0.133
rrs1473163r.1318c>t0.133
rrs1473164r.1319c>a0.133
rrs1473166r.1321g>a0.129
rrs1473172r.1327t>c0.130
rrs1473173r.1328c>t0.130
rrs1473177r.1332g>a0.133
rrs1473191r.1346c>t0.127
rrs1473202r.1357c>t0.117
rrs1473206r.1361g>a0.132
rrs1473226r.1381c>t0.139
rrs1473352r.1507c>t0.110
rrl1474387r.730c>t0.214
rrl1474839r.1182c>t0.155
rrl1474844r.1187g>t0.155
rrl1474864r.1207c>t0.154
rrl1474866r.1209c>a0.154
rrl1474869r.1212g>t0.154
rrl1474892r.1235g>a0.156
rrl1474896r.1239a>g0.158
rrl1474902r.1245t>c0.160
rrl1474903r.1246t>a0.160
rrl1474904r.1247g>c0.160
rrl1474913r.1256t>a0.162
rrl1474920r.1263g>c0.162
rrl1475574r.1917c>a0.248
rrl1475803r.2146t>c0.227
rrl1475804r.2147g>c0.227
rrl1475816r.2159c>g0.270
rrl1475817r.2160a>g0.274
rrl1475858r.2201t>c0.277
rrl1475866r.2209t>a0.267
rrl1476225r.2568t>g0.207
rrl1476229r.2572c>t0.214
rrl1476260r.2603a>g0.225
rrl1476268r.2611a>t0.215
rrl1476275r.2618t>a0.218
rrl1476279r.2622g>a0.200
rrl1476280r.2623a>c0.200
rrl1476293r.2636c>t0.167
rrl1476294r.2637a>g0.138
rrl1476295r.2638c>g0.138
rrl1476296r.2639c>t0.141
rrl1476297r.2640c>t0.141
rrl1476301r.2644a>c0.139
rrl1476302r.2645g>a0.138
rrl1476311r.2654g>c0.156
rrl1476312r.2655t>c0.160
rrl1476313r.2656g>a0.160
rrl1476332r.2675g>c0.279
rrl1476353r.2696g>t0.302
rrl1476358r.2701t>c0.310
rrl1476369r.2712c>t0.300
rrl1476372r.2715t>c0.300
rrl1476382r.2725a>g0.286
rrl1476383r.2726t>a0.289
rrl1476408r.2751g>a0.308
rrl1476425r.2768g>t0.309
rrl1476428r.2771c>t0.312
rrl1476429r.2772a>c0.319
rrl1476466r.2809c>t0.369
rrl1476481r.2824t>c0.330
rrl1476506r.2849t>c0.242
rrl1476514r.2857c>t0.190
rrl1476517r.2860c>t0.167
rrl1476519r.2862c>g0.167
rrl1476524r.2867c>a0.167
rrl1476525r.2868a>g0.167
rrl1476530r.2873c>t0.161
rrl1476536r.2879g>a0.161
rrl1476537r.2880a>g0.161
rrl1476538r.2881a>g0.159
rrl1476540r.2883c>g0.169
rrl1476547r.2890c>t0.184
rrl1476567r.2910c>t0.189
rrl1476572r.2915g>a0.187
rrl1476573r.2916a>t0.191
rrl1476584r.2927c>t0.180
tlyA1917972c.33A>G1.000
alr3841652c.-232A>T0.298
alr3841654c.-234A>C0.303
alr3841662c.-242A>G0.381
alr3841663c.-243G>A0.305
embA4244211p.Pro327Ser1.000

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;