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: 5d4009a02d7d8
Sample: 5d4009a02d7d8

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Summary
ID: 5d4009a02d7d8
Date: Tue Jul 30 10:12:11 2019
Strain: lineage4.3;lineage1.2.2;lineage4.1.1;lineage1.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage1.2.2Indo-OceanicEAI1RD239
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage1.1.1Indo-OceanicEAI4;EAI5RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6811c.1572C>T1.000
gyrA9323c.2022C>A1.000
rpoB759606c.-201T>C1.000
rpoB760406c.600G>C1.000
rpoB760412c.606C>G1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoC763675c.306C>G1.000
rpoC763696c.327T>C1.000
rpoC763702c.333C>G1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C1.000
rpoC763732c.363C>G1.000
rpoC763741c.372C>T1.000
rpoC763744c.375G>C1.000
rpoC763765c.396T>C1.000
rpoC763774c.405G>C1.000
rpoC763807c.438T>C1.000
rpoC764752c.1383G>C1.000
rpoC764764c.1395T>C1.000
rpoC764827c.1458G>C1.000
rpoC766804c.3435A>G1.000
rplC801180c.372C>G1.000
rplC801195c.387G>C1.000
rplC801207c.399C>T1.000
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471969r.124t>c1.000
rrs1471970r.125g>a1.000
rrs1472075r.230a>g1.000
rrs1472333r.488g>a0.312
rrs1472339r.494c>t0.526
rrs1472344r.499c>t0.435
rrs1472349r.504a>c0.286
rrs1472374r.529t>g0.243
rrs1472378r.533g>a0.417
rrs1472379r.534t>g0.343
rrs1472382r.537g>a0.333
rrs1472389r.544g>a0.441
rrs1472396r.551a>t0.500
rrs1472400r.555c>t0.480
rrs1472537r.692c>t0.552
rrs1472544r.699c>a0.516
rrs1472545r.700a>t0.516
rrs1472549r.704g>a0.484
rrs1472557r.712g>a0.516
rrs1472571r.726g>c0.516
rrs1472573r.728c>g0.258
rrs1472579r.734g>t0.552
rrs1472581r.736a>t0.552
rrs1472583r.738t>c0.244
rrs1472598r.753a>c0.828
rrs1472599r.754g>a0.779
rrs1472607r.762g>a0.196
rrs1472612r.767g>t0.674
rrs1472614r.769g>t0.526
rrs1472616r.771g>a0.137
rrs1472634r.789t>c0.381
rrs1472635r.790g>a0.368
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473105r.1260g>a1.000
rrs1473120r.1275c>ct1.000
rrs1473123r.1278a>t1.000
rrs1473145r.1300c>t1.000
rrs1473166r.1321g>a1.000
rrl1473756r.99g>a1.000
rrl1473758r.101g>t1.000
rrl1473806r.149c>t1.000
rrl1473877r.220g>a1.000
rrl1473898r.241c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473986r.329t>c1.000
rrl1473987r.330g>a1.000
rrl1473995r.338g>t1.000
rrl1474001r.344c>t1.000
rrl1474009r.352a>g1.000
rrl1474012r.355c>t1.000
rrl1474093r.436g>t1.000
rrl1474099r.442g>a1.000
rrl1474103r.446a>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474249r.592g>t1.000
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474356r.699t>c1.000
rrl1474362r.705a>g1.000
rrl1474376r.719t>c1.000
rrl1474639r.982g>a1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474823r.1166c>t1.000
rrl1474831r.1174a>g1.000
rrl1475291r.1634a>c1.000
rrl1475313r.1656g>a1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>t1.000
rrl1475402r.1745c>t1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>a1.000
rrl1475436r.1779c>t1.000
rrl1475483r.1826c>t1.000
rrl1475505r.1848g>a1.000
rrl1475642r.1985t>c1.000
rrl1475657r.2000a>g1.000
rrl1475659r.2002g>t1.000
rrl1475881r.2224t>c1.000
rrl1475988r.2331a>g1.000
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476608r.2951c>g1.000
rrl1476628r.2971t>a1.000
fabG11673535c.96A>G1.000
fabG11673547c.108T>C1.000
fabG11673568c.129C>G1.000
fabG11673574c.135C>G1.000
fabG11673580c.141T>G1.000
fabG11673589c.150A>G1.000
fabG11673595c.156A>C1.000
fabG11673596p.Lys53Glu1.000
fabG11673601c.162G>C1.000
fabG11673602c.163C>T1.000
fabG11673607c.168T>C1.000
fabG11673615p.Glu59Val1.000
fabG11673619c.180T>C1.000
fabG11673633p.Ser65Asn1.000
fabG11673637p.Asp66Glu1.000
fabG11673641p.Val68Ile1.000
fabG11673646c.207T>C1.000
fabG11673657p.Thr73Lys1.000
fabG11673660p.Ala74Glu1.000
fabG11673664c.225A>C1.000
fabG11673667c.228A>G1.000
fabG11673679c.240T>C1.000
fabG11673685c.246C>T1.000
fabG11673716p.Ala93Lys1.000
fabG11673733p.Met98Ile1.000
fabG11673941p.Ala168Ser1.000
fabG11673946c.507C>G1.000
rpsA1833554p.Thr5Ala1.000
embC4240789c.927T>C1.000
embC4240819c.957A>G1.000
embC4240828c.966G>A1.000
embC4240831c.969T>G1.000
embC4241449c.1587C>G1.000
embC4241453p.Ile531Val1.000
embC4241479c.1617C>G1.000
embC4241480c.1618T>C1.000
embC4241488c.1626G>C1.000
embA4244498c.1266A>G1.000
embA4244507c.1275G>T1.000
embA4244508c.1276T>C1.000
embA4244516c.1284G>C1.000
embA4244517p.Leu429Val1.000
embA4244523p.Pro431Ala1.000
embA4244534c.1302T>C1.000
embA4244537c.1305T>G1.000
embA4244543c.1311C>G1.000
embA4244547p.Ile439Val1.000
embA4244557p.Arg442Thr1.000
embA4244582c.1350T>C1.000
embA4244585c.1353A>G1.000

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;