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.
Back to results page.
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: 5c802cf2758b7
Sample: 5c802cf2758b7

Summary
ID: 5c802cf2758b7
Date: Wed Mar 6 20:28:13 2019
Strain: lineage4.4.1.1
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.4Euro-AmericanS;TNone
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.1Euro-AmericanS;OrphansNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA736221E>21Q1.000
gyrA758595S>95T1.000
gyrA8710470A>470E0.988
gyrA91131812C>T1.000
gyrA9304668G>668D1.000
rrs1472517672T>C0.118
rrs1472530685G>A0.346
rrs1472537692C>T0.176
rrs1472571726G>C0.268
rrs1472581736A>C0.295
rrs1472583738T>G0.140
rrs1472584739A>T0.200
rrs1472594749G>A0.115
rrs1472597752G>A0.132
rrs1472598753A>C0.312
rrs1472616771G>A0.255
rrs1472634789T>C0.116
rrs1472648803G>C0.176
rrs1472714869A>G0.214
rrs1472715870C>T0.167
rrs1472716871C>A0.175
rrs1472734889C>T0.186
rrs1472741896G>A0.178
rrs1472742897C>T0.205
rrs1472759914T>A0.178
rrs1472767922G>A0.238
rrs1472781936C>T0.238
rrs1472793948A>T0.256
rrs1472803958T>A0.231
rrs1472805960C>A0.200
rrs1472806961A>T0.200
rrs14728871042G>C0.160
rrs14728921047T>C0.176
rrs14728951050C>T0.135
rrl1474197540C>T0.143
rrl1474467810A>T0.182
rrl1474497840G>C0.200
rrl1474506849C>G0.200
rrl1474507850G>T0.200
rrl1474582925T>A0.200
rrl1474636979A>T0.200
rrl1474637980C>T0.200
rrl1474638981C>G0.200
rrl1474639982G>T0.200
rrl1474640983C>T0.200
rrl14746621005C>T0.167
rrl14746661009T>G0.167
rrl14746701013C>G0.167
rrl14746721015C>T0.167
rrl14746751018C>T0.167
rrl14747491092C>T0.188
rrl14747601103A>G0.294
rrl14747941137C>T0.250
rrl14748231166C>G0.231
rrl14748241167A>G0.231
rrl14748251168G>A0.154
rrl14748301173A>T0.182
rrl14748311174A>T0.250
rrl14748521195T>C0.154
rrl14758032146T>C0.156
rrl14758042147G>C0.156
rrl14758162159C>G0.176
rrl14758172160A>G0.206
rrl14758772220C>T0.150
rrl14758812224T>C0.150
rrl14758832226A>T0.150
rrl14758922235A>C0.150
rrl14763222665C>A0.256
rrl14763582701T>C0.383
rrl14763682711T>C0.367
rrl14763692712C>T0.388
rrl14763722715T>C0.388
rrl14763822725A>G0.360
rrl14763832726T>A0.360
rrl14764082751G>A0.367
rrl14764422785T>A0.292
rrl14764432786G>T0.277
rrl14764552798C>A0.325
rrl14764562799A>T0.325
rrl14764662809C>T0.324
rrl14764812824T>C0.359
rrl14765062849T>C0.211
tlyA191797233A>G1.000
embC42426432781C>T1.000

Analysis pipeline specifications

TBProfiler Version: 0.1

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;