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: 5d70cc471125e
Sample: 5d70cc471125e

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Summary
ID: 5d70cc471125e
Date: Thu Sep 5 09:52:57 2019
Strain: lineage4.3.4.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (0.98), ahpC c.-52C>T (1.00)
RifampicinRrpoB p.Ser450Leu (0.92)
EthambutolRembA c.-16C>T (0.97), embB p.Met306Leu (0.95)
PyrazinamideRpncA c.419 419del (1.00)
StreptomycinRrpsL p.Lys43Arg (0.96)
EthionamideRethA c.32 32del (0.99)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6140p.Val301Leu0.957
gyrB6745c.1506T>C0.125
gyrB6751c.1512G>C0.125
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA7763c.462T>C0.120
gyrA7781c.480G>C0.120
gyrA7784c.483A>G0.122
gyrA7793c.492G>C0.136
gyrA7799c.498A>G0.115
gyrA8795c.1494C>T0.947
gyrA9304p.Gly668Asp1.000
gyrA9374c.2073G>C0.118
gyrA9377c.2076A>G0.116
rpoC764059c.690G>T0.139
rpoC764083c.714A>G0.168
rpoC764098c.729A>G0.178
rpoC764101c.732C>G0.170
rpoC764102p.Val245Ile0.170
rpoC764110c.741C>G0.165
rpoC764112p.Tyr248Phe0.160
rpoC764116c.747C>T0.160
rpoC764131c.762T>C0.200
rpoC764140c.771C>T0.214
rpoC764188c.819A>G0.206
rpoC764195p.Ser276Ile0.154
rpoC764203c.834G>C0.147
rpoC764206c.837T>C0.147
rpoC764215c.846A>G0.155
rpoC764257c.888G>C0.175
rpoC764266c.897T>C0.129
rpoC764353c.984G>T0.142
rpoC764365c.996C>T0.147
rpoC764387c.1018T>C0.124
rpoC764703p.Lys445Arg0.907
rpoC764995c.1626C>G1.000
rpoC765613p.His748Gln0.123
rpoC765625c.2256C>G0.128
rpoC765631p.Asp754Glu0.120
rpoC766894c.3525T>C0.133
rpoC766895c.3526T>C0.135
rpoC766963c.3594T>C0.121
rpoC766972c.3603G>C0.133
rpoC766975c.3606C>T0.137
rpoC766996c.3627C>T0.116
rpoC767009c.3640T>A0.121
rpsL781395c.-165T>C1.000
rrl1475881r.2224t>c0.135
fabG11673941p.Ala168Ser0.127
fabG11673955c.516G>C0.124
fabG11673985c.546C>G0.118
rpsA1834195c.654G>C0.126
rpsA1834222c.681T>C0.142
tlyA1917972c.33A>G1.000
thyX3067685c.261T>G0.117
thyX3067694c.252C>G0.117
thyX3067718c.228G>C0.137
thyX3067721c.225A>G0.140
thyX3067736c.210G>A0.126
thyX3067739c.207A>G0.127
thyX3067742c.204T>C0.127
thyA3073868p.Thr202Ala0.958
ald3086788c.-32T>C1.000
alr3840719c.702T>C1.000
embC4242643c.2781C>T0.980
embA4245113c.1881C>G0.123
gid4408156p.Leu16Arg1.000

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;