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: 5c8258b023565
Sample: 5c8258b023565

Summary
ID: 5c8258b023565
Date: Fri Mar 8 12:00:57 2019
Strain: lineage2.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB 306M>306I (0.90)
Pyrazinamide
Streptomycin
EthionamideRethA 381A>381P (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rpoB7628941030L>1030M0.250
rpoB7629203114C>T0.300
rpoB7631093303C>G0.250
rpoB7631153309T>C0.250
rpoB7631221106I>1106V0.273
rpoB7631371111I>1111V0.300
rpoB7631423336C>G0.300
rpoC76342419D>19Y0.200
rpoC763486117T>C0.357
rpoC76350144D>44E0.455
rpoC763504135C>G0.455
rpoC763507138G>C0.455
rpoC763525156C>T0.385
rpoC763528159G>C0.417
rpoC763534165T>C0.455
rpoC76353556R>56K0.455
rpoC763540171C>T0.500
rpoC76355061Y>61H0.611
rpoC763570201G>C0.600
rpoC763573204G>C0.600
rpoC76357870F>70Y0.600
rpoC763582213G>A0.562
rpoC76358673I>73V0.562
rpoC76358974I>74V0.600
rpoC76359776E>76D0.632
rpoC763609240C>T0.286
rpoC763612243G>A0.333
rpoC763615246G>C0.364
rpoC763621252C>T0.429
rpoC763627258G>A0.429
rpoC763633264T>C0.400
rpoC763636267T>C0.400
rpoC763642273G>C0.444
rpoC763648279C>A0.412
rpoC763666297G>T0.200
rpoC763669300C>T0.188
rpoC763673102T>102S0.200
rpoC763678309C>T0.200
rpoC7644051036A>C0.400
rpoC7644101041G>C0.400
rpoC7644281059G>T0.333
rpoC7644851116G>C0.250
rpoC7646051236G>T0.176
rpoC7646201251G>T0.158
rrs14718527T>A0.500
rrs147189651T>C0.933
rrs147190055C>T0.930
rrs147191469A>G0.610
rrs147191974A>T0.240
rrs1472089244C>T0.500
rrs1472094249T>A0.692
rrs1472106261G>A0.956
rrs1472112267C>T0.942
rrs1472113268T>C0.958
rrs1472127282C>T0.974
rrs1472129284G>C0.975
rrs1472137292G>A0.973
rrs1472150305T>A0.991
rrs1472151306C>T0.992
rrs1472172327T>C0.996
rrs1472203358G>A0.958
rrs1472210365A>C0.908
rrs1472213368G>C0.895
rrs1472215370A>G0.895
rrs1472222377G>A0.859
rrs1472229384C>T0.824
rrs1472234389T>C0.815
rrs1472236391C>G0.812
rrs1472240395G>A0.800
rrs1472251406G>A0.600
rrs1472253408G>T0.576
rrs1472256411T>G0.576
rrs1472259414C>A0.559
rrs1472271426T>C0.484
rrs1472277432C>G0.250
rrs1472333488G>A0.310
rrs1472338493A>C0.855
rrs1472344499C>T0.965
rrs1472379534T>G0.983
rrs1472382537G>A0.982
rrs1472400555C>T0.975
rrs1472517672T>A0.915
rrs1472518673G>C0.906
rrs1472530685G>A0.917
rrs1472537692C>T0.898
rrs1472541696T>G0.905
rrs1472544699C>G0.892
rrs1472545700A>T0.899
rrs1472557712G>A0.950
rrs1472570725G>A0.922
rrs1472571726G>C0.927
rrs1472573728C>T0.935
rrs1472581736A>T0.945
rrs1472598753A>C0.957
rrs1472616771G>A0.958
rrs1472716871C>T0.391
rrs1472733888G>C0.944
rrs1472734889C>T0.936
rrs1472741896G>A0.944
rrs1472742897C>G0.951
rrs1472744899A>G0.952
rrs1472767922G>A0.961
rrs1472779934G>A0.920
rrs1472781936C>T0.934
rrs1472786941C>T0.935
rrs1472793948A>T0.955
rrs1472803958T>A0.958
rrs14728951050C>T0.957
rrs14729541109T>A0.400
rrs14730201175T>C0.976
rrs14730351190G>A0.972
rrs14730531208T>A0.949
rrs14730561211A>T0.950
rrs14730621217T>A0.947
rrs14730681223A>G0.948
rrs14730701225G>A0.951
rrs14730891244A>C0.916
rrs14730941249T>C0.915
rrs14730991254T>A0.906
rrs14731091264T>C0.877
rrs14731101265T>G0.877
rrs14731111266A>G0.877
rrs14731151270G>C0.884
rrs14731451300C>T0.816
rrs14731471302G>C0.806
rrs14731481303G>A0.806
rrs14731501305T>G0.817
rrs14731611316A>C0.811
rrs14731631318C>T0.811
rrs14731641319C>G0.811
rrs14731661321G>A0.849
rrs14731771332G>A0.944
rrs14731791334C>T0.944
rrs14731921347A>G0.953
rrs14732021357C>T0.953
rrs14732051360T>C0.954
rrs14732261381C>T0.964
rrs14733271482A>G0.667
rrs14733281483C>T0.682
rrs14733521507C>T0.959
rrl147372568G>A0.214
rrl147373174T>G0.804
rrl147375093C>G0.804
rrl147375295G>A0.810
rrl1473758101G>T0.831
rrl1473765108A>G0.855
rrl1473851194G>C0.346
rrl1473862205C>A0.400
rrl1473870213G>T0.389
rrl1473871214T>G0.389
rrl1473876219G>A0.378
rrl1473887230T>A0.587
rrl1473888231T>C0.587
rrl1473898241C>T0.562
rrl1473899242A>C0.600
rrl1473905248T>C0.587
rrl1474218561T>A0.927
rrl1474228571T>C0.930
rrl1474232575C>G0.921
rrl1474239582G>C0.906
rrl1474249592G>T0.897
rrl1474252595T>A0.897
rrl1474330673A>T0.913
rrl1474338681G>A0.585
rrl1474341684T>G0.467
rrl1474348691C>T0.238
rrl1474587930G>A0.344
rrl14747791122G>A0.909
rrl14747801123C>T0.909
rrl14747821125G>A0.913
rrl14747901133C>T0.933
rrl14747981141C>T0.935
rrl14748041147C>T0.943
rrl14748231166C>G0.914
rrl14748271170C>T0.915
rrl14748301173A>C0.920
rrl14748311174A>C0.921
rrl14748441187G>T0.962
rrl14748661209C>A0.961
rrl14748691212G>T0.965
rrl14748961239A>G0.950
rrl14749021245T>C0.948
rrl14749041247G>C0.947
rrl14749131256T>A0.946
rrl14749201263G>A0.937
rrl14749281271C>A0.375
rrl14749311274G>A0.643
rrl14749381281G>A0.360
rrl14751221465C>T0.902
rrl14751291472G>A0.912
rrl14751541497C>A0.926
rrl14751671510T>A0.919
rrl14751751518G>A0.922
rrl14751881531C>T0.911
rrl14754981841C>G0.954
rrl14755501893A>C0.440
rrl14755521895G>C0.533
rrl14755701913A>C0.943
rrl14755741917C>A0.936
rrl14756722015C>G0.965
rrl14756732016T>C0.957
rrl14756872030C>T0.958
rrl14756962039T>C0.953
rrl14756992042C>T0.963
rrl14757032046A>G0.965
rrl14757072050T>A0.966
rrl14757162059A>G0.966
rrl14757472090A>G0.679
rrl14758032146T>C0.945
rrl14758042147G>C0.947
rrl14758162159C>G0.963
rrl14758172160A>G0.964
rrl14758432186G>A0.943
rrl14758492192G>A0.943
rrl14758532196C>T0.945
rrl14758582201T>C0.947
rrl14761222465A>C0.409
rrl14761262469C>T0.409
rrl14761282471T>A0.519
rrl14761352478T>C0.908
rrl14761412484A>G0.922
rrl14761532496T>C0.937
rrl14761942537A>G0.227
rrl14762212564T>C0.222
rrl14762252568T>G0.562
rrl14762292572C>T0.735
rrl14762512594T>C0.946
rrl14762602603A>G0.953
rrl14762802623A>C0.957
rrl14762932636C>T0.825
rrl14762942637A>G0.821
rrl14762952638C>G0.821
rrl14762962639C>T0.800
rrl14762972640C>A0.800
rrl14763022645G>A0.800
rrl14763112654G>C0.762
rrl14763122655T>C0.762
rrl14763132656G>A0.745
rrl14763322675G>C0.940
rrl14763382681C>T0.941
rrl14763532696G>T0.947
rrl14763582701T>C0.948
rrl14763722715T>C0.942
rrl14763822725A>G0.918
rrl14763832726T>A0.928
rrl14764082751G>A0.963
rrl14764252768G>A0.969
rrl14764282771C>T0.969
rrl14764662809C>T0.970
rrl14764812824T>C0.961
rrl14765062849T>C0.928
rrl14765122855C>T0.389
rrl14765402883C>G0.294
rrl14765472890C>T0.923
rrl14765672910C>T0.952
rrl14765732916A>T0.951
rrl14765772920T>G0.948
rrl14765842927C>T0.953
rrl14765942937C>T0.951
rrl14766032946G>A0.952
rrl14766142957A>G0.936
rrl14766192962C>T0.930
rrl14766242967T>A0.926
rrl14766282971T>A0.926
rrl14766302973A>G0.926
rrl14766372980C>G0.942
rrl14766573000G>C0.316
pncA2288724518T>TC0.688
gid4407588615T>C0.909
gid440792792E>92D1.000

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;