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: 5ddd18bdecd56
Sample: 5ddd18bdecd56

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Summary
ID: 5ddd18bdecd56
Date: Tue Nov 26 12:22:33 2019
Strain: lineage4.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRfabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00), rpoC p.Gly332Arg (1.00)
EthambutolRembA c.-16C>T (1.00), embB p.Asp328Tyr (1.00)
PyrazinamideRpncA c.393 394insGG (1.00)
StreptomycinRrrs r.514a>c (0.59)
EthionamideRfabG1 c.-15C>T (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6507p.Ala423Val1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
gyrA9656c.2355C>G1.000
rpoB762254c.2448T>C0.200
rpoB762257c.2451C>G0.200
rpoC765150p.Gly594Glu1.000
rpoC765187c.1818C>T1.000
rpoC766012c.2643C>G1.000
rpsL781395c.-165T>C1.000
rpsL781421c.-139C>A1.000
embR1416935p.Leu138Arg0.250
rrs1472009r.164t>g0.273
rrs1472235r.390g>c0.200
rrs1472240r.395g>a0.200
rrs1472242r.397c>t0.200
rrs1472344r.499c>t0.200
rrs1472378r.533g>t0.267
rrs1472379r.534t>g0.286
rrs1472382r.537g>a0.308
rrs1472389r.544g>a0.200
rrs1472396r.551a>t0.200
rrs1472400r.555c>t0.333
rrs1472507r.662c>a0.200
rrs1472518r.673g>a0.200
rrs1472530r.685g>a0.200
rrs1472537r.692c>t0.231
rrs1472544r.699c>t0.143
rrs1472557r.712g>a0.217
rrs1472767r.922g>c0.308
rrs1472790r.945t>c0.250
rrs1472865r.1020c>t0.200
rrs1472866r.1021c>t0.200
rrs1472878r.1033g>t0.167
rrs1472879r.1034t>c0.167
rrs1472880r.1035g>a0.167
rrs1473226r.1381c>t0.174
rrs1473352r.1507c>t0.357
rrl1474628r.971c>t0.200
rrl1475817r.2160a>g0.158
rrl1476194r.2537a>g0.200
rrl1476200r.2543a>t0.200
rrl1476214r.2557g>t0.200
rrl1476215r.2558c>t0.200
rrl1476336r.2679c>t0.500
rrl1476338r.2681c>t0.500
rrl1476356r.2699c>g0.300
rrl1476357r.2700t>a0.300
rrl1476358r.2701t>c1.000
rrl1476359r.2702c>g0.583
rrl1476369r.2712c>t0.636
rrl1476381r.2724g>c0.538
rrl1476382r.2725a>g0.538
rrl1476383r.2726t>g0.538
rrl1476384r.2727g>t0.538
rrl1476408r.2751g>a0.294
rrl1476411r.2754g>t0.312
rrl1476425r.2768g>t0.333
rrl1476428r.2771c>t0.357
rrl1476429r.2772a>c0.333
rrl1476442r.2785t>a0.278
rrl1476443r.2786g>t0.294
rrl1476455r.2798c>a0.333
rrl1476456r.2799a>t0.312
rrl1476463r.2806c>a0.333
rrl1476466r.2809c>t0.375
rrl1476470r.2813c>t0.375
rrl1476483r.2826g>a0.312
rrl1476506r.2849t>c0.455
rrl1476567r.2910c>t0.250
rrl1476573r.2916a>t0.214
inhA1674828p.Glu209Asp0.182
tlyA1917972c.33A>G1.000
katG2155278c.834G>A0.174
katG2155824c.288G>A1.000
katG2156007c.105G>A1.000
folC2746779p.Gly274Ser0.150
ribD2987210c.373 374insCGC0.167
ald3086788c.-32T>C1.000
embC4241033p.Pro391Ser0.160
embC4242643c.2781C>T1.000
embC4242803p.Val981Leu1.000
embA4244262c.1030C>T1.000
ethA4327431p.Ser15Pro1.000
gid4407980p.Pro75Ser1.000

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;