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: 5d6b665727d4f
Sample: 5d6b665727d4f

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Summary
ID: 5d6b665727d4f
Date: Sun Sep 1 07:35:26 2019
Strain: lineage2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1401a>g (0.91)
CapreomycinRrrs r.1401a>g (0.91)
KanamycinRrrs r.1401a>g (0.91)

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA8375c.1074G>C0.200
gyrA8399c.1098T>C0.200
gyrA8903c.1602T>C0.200
gyrA8933c.1632G>A0.200
gyrA8939c.1638T>C0.200
gyrA8942c.1641G>C0.200
gyrA8945c.1644G>T0.200
gyrA8946c.1645T>C0.200
gyrA8981c.1680G>C0.200
rpoB761219c.1413G>T0.200
rpoB761261c.1455G>T0.200
rpoB761282c.1476C>A0.200
rpoB763028c.3222T>C0.273
rpoB763031c.3225T>C0.273
rpoB763034c.3228C>G0.273
rpoB763040c.3234C>G0.273
rpoB763043c.3237G>A0.300
rpoC764749c.1380G>C0.273
rpoC764752c.1383G>C0.273
rpoC764764c.1395T>C0.250
rpoC764911c.1542A>G0.200
rpoC764918p.Val517Ile0.200
rpoC764923c.1554A>G0.200
rpsL781395c.-165T>C1.000
rpsL781586c.27C>A0.200
rpsL781608p.Ser17Ala0.182
rpsL781631c.72G>C0.182
rpsL781649c.90T>C0.182
rpsL781655c.96T>C0.182
rpsL781658c.99A>G0.182
rplC800901c.93C>A0.200
rplC800907c.99C>G0.200
rplC800913c.105G>C0.182
rplC800916c.108A>G0.182
rplC800919c.111C>G0.250
rplC800934c.126C>G0.250
rplC800937c.129A>G0.250
rplC800985c.177A>C0.200
rrs1471969r.124t>c0.200
rrs1471970r.125g>a0.182
rrs1471984r.139t>a0.200
rrs1471985r.140t>c0.200
rrs1472030r.185g>t0.167
rrs1472031r.186g>t0.167
rrs1472033r.188a>g0.167
rrs1473120r.1275c>ct0.286
rrs1473123r.1278a>t0.267
rrl1474034r.377g>a0.200
rrl1474083r.426c>t0.200
rrl1474181r.524c>t0.182
rrl1474201r.544t>a0.200
rrl1475061r.1404c>t0.188
rrl1475526r.1869c>a0.300
rrl1475988r.2331a>g0.167
rpsA1834690c.1149T>C0.200
thyX3067814c.132A>G0.200
thyX3067820c.126G>C0.200
thyX3067832c.114G>A0.200
thyX3067849p.Pro33Ser0.200
thyX3067850c.96T>G0.200
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.300
alr3841654c.-234A>C0.304
embA4245077c.1845G>A0.200
embA4245101c.1869G>C0.200
ethA4326613c.861G>A0.200
ethA4326646c.828G>A0.200
ethA4326649c.825C>A0.200
ethA4326652c.822C>T0.182
ethA4326658c.816T>A0.182
ethA4326874p.Lys200Asn0.200
ethA4326886c.588G>A0.200
ethA4326892c.582C>A0.200
ethA4326895c.579C>T0.273
ethA4326901c.573C>A0.250
ethA4326907c.567C>A0.308
ethA4326913c.561C>G0.308
ethA4326919c.555T>G0.364
ethA4326950p.Ala175Gly0.400

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;