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: 5d4a6fe8996b2
Sample: 5d4a6fe8996b2

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Summary
ID: 5d4a6fe8996b2
Date: Wed Aug 7 07:34:46 2019
Strain: lineage2.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.His445Tyr (1.00)
EthambutolRembB p.Met306Val (1.00)
PyrazinamideRpncA p.Lys96Glu (1.00)
StreptomycinRrpsL p.Lys88Arg (1.00)
EthionamideRethA c.754 755insG (0.99)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpoC766824p.Lys1152Arg0.993
rpsL781395c.-165T>C1.000
rrs1471892r.47g>a0.203
rrs1471893r.48t>g0.190
rrs1472164r.319g>a0.239
rrs1472172r.327t>c0.272
rrs1472177r.332c>t0.291
rrs1472240r.395g>c0.280
rrs1472242r.397c>t0.277
rrs1472251r.406g>t0.175
rrs1472252r.407g>a0.175
rrs1472253r.408g>t0.172
rrs1472256r.411t>a0.174
rrs1472259r.414c>a0.165
rrs1472344r.499c>t0.260
rrs1472349r.504a>c0.270
rrs1472374r.529t>g0.312
rrs1472382r.537g>a0.343
rrs1472389r.544g>a0.290
rrs1472390r.545t>a0.290
rrs1472391r.546c>t0.290
rrs1472594r.749g>c0.228
rrs1472598r.753a>t0.244
rrs1472616r.771g>a0.306
rrs1472742r.897c>t0.240
rrs1472754r.909g>t0.245
rrs1472781r.936c>t0.287
rrs1472793r.948a>t0.263
rrs1472887r.1042g>c0.212
rrs1472912r.1067c>t0.229
rrs1472917r.1072g>a0.256
rrs1473044r.1199c>g0.228
rrs1473051r.1206t>c0.218
rrs1473053r.1208t>a0.218
rrs1473062r.1217t>a0.254
rrs1473068r.1223a>g0.199
rrs1473163r.1318c>t0.188
rrs1473166r.1321g>a0.189
rrs1473177r.1332g>a0.243
rrs1473191r.1346c>t0.215
rrs1473192r.1347a>g0.235
rrs1473202r.1357c>t0.225
rrs1473205r.1360t>c0.227
rrs1473206r.1361g>a0.210
rrl1474582r.925t>c0.153
rrl1474584r.927c>g0.152
rrl1474837r.1180a>g0.228
rrl1474844r.1187g>t0.238
rrl1474864r.1207c>t0.219
rrl1474866r.1209c>a0.206
rrl1474869r.1212g>t0.220
rrl1474875r.1218g>a0.246
rrl1474876r.1219t>a0.251
rrl1475526r.1869c>a0.297
rrl1475538r.1881t>c0.168
rrl1475539r.1882a>t0.168
rrl1475540r.1883c>t0.160
rrl1475545r.1888t>g0.158
rrl1475550r.1893a>c0.160
rrl1475551r.1894t>g0.167
rrl1475555r.1898t>g0.157
rrl1475564r.1907c>a0.262
rrl1475574r.1917c>g0.270
rrl1475575r.1918c>t0.270
rrl1475576r.1919c>g0.270
rrl1475791r.2134a>g0.190
rrl1475803r.2146t>c0.218
rrl1475804r.2147g>c0.221
rrl1475816r.2159c>g0.275
rrl1475817r.2160a>g0.290
rrl1476336r.2679c>t0.356
rrl1476356r.2699c>a0.232
rrl1476357r.2700t>c0.234
rrl1476358r.2701t>c0.238
rrl1476359r.2702c>g0.247
rrl1476369r.2712c>t0.272
rrl1476381r.2724g>c0.254
rrl1476382r.2725a>g0.254
rrl1476383r.2726t>g0.259
rrl1476384r.2727g>t0.263
rrl1476408r.2751g>a0.391
rrl1476411r.2754g>a0.389
rrl1476425r.2768g>a0.368
rrl1476428r.2771c>t0.362
rrl1476442r.2785t>a0.357
rrl1476443r.2786g>t0.355
rrl1476455r.2798c>a0.332
rrl1476456r.2799a>t0.332
rrl1476463r.2806c>t0.335
rrl1476466r.2809c>t0.358
rrl1476506r.2849t>c0.303
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
ethA4326994c.480C>A1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;