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: 5da4955c1b9ca
Sample: 5da4955c1b9ca

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Summary
ID: 5da4955c1b9ca
Date: Mon Oct 14 16:39:58 2019
Strain: lineageBOV
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineageBOVM. bovisBOV 1;BOV 2None
lineageBOV AFRI???

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6406c.1167C>T1.000
gyrB6446p.Ala403Ser1.000
gyrA8285c.984C>T1.000
gyrA9143c.1842T>C1.000
rpoC764936p.Gln523Lys0.200
Rv0678779090p.Arg34Pro0.200
rpsL781717p.Ala53Asp0.200
rplC800965p.Ala53Pro0.364
embR1416222p.Phe376Leu0.444
embR1416234p.Cys372Gly0.556
rrs1471900r.55c>t0.981
rrs1471914r.69a>g0.800
rrs1472102r.257g>a0.882
rrs1472106r.261g>a0.912
rrs1472113r.268t>c0.919
rrs1472127r.282c>t0.925
rrs1472137r.292g>a0.929
rrs1472150r.305t>a0.941
rrs1472172r.327t>c0.952
rrs1472203r.358g>a0.934
rrs1472210r.365a>t0.951
rrs1472213r.368g>c0.951
rrs1472215r.370a>g0.951
rrs1472225r.380c>a1.000
rrs1472234r.389t>c0.939
rrs1472236r.391c>g0.906
rrs1472240r.395g>a1.000
rrs1472251r.406g>a1.000
rrs1472256r.411t>a0.911
rrs1472259r.414c>a0.911
rrs1472262r.417c>t0.886
rrs1472269r.424g>a0.886
rrs1472271r.426t>c0.886
rrs1472344r.499c>t0.636
rrs1472378r.533g>t0.904
rrs1472379r.534t>g0.922
rrs1472412r.567a>g0.571
rrs1472489r.644a>ag0.818
rrs1472490r.645g>gt0.818
rrs1472517r.672t>c0.231
rrs1472518r.673g>a0.231
rrs1472530r.685g>a0.462
rrs1472537r.692c>t0.462
rrs1472544r.699c>t0.308
rrs1472545r.700a>g0.231
rrs1472557r.712g>a0.357
rrs1472570r.725g>a0.231
rrs1472571r.726g>c0.308
rrs1472573r.728c>t0.250
rrs1472579r.734g>a0.231
rrs1472583r.738t>c0.273
rrs1472598r.753a>c0.600
rrs1472607r.762g>t0.375
rrs1472608r.763t>a0.353
rrs1472616r.771g>a0.769
rrs1472620r.775a>g0.385
rrs1472634r.789t>c0.583
rrs1472705r.860g>a0.800
rrs1472708r.863t>a1.000
rrs1472742r.897c>t0.966
rrs1472744r.899a>g0.966
rrs1472781r.936c>t0.976
rrs1472793r.948a>t0.990
rrs1472803r.958t>a0.981
rrs1472824r.979t>a0.680
rrs1472827r.982g>t0.500
rrs1472828r.983t>c0.500
rrs1472951r.1106t>c0.606
rrs1472967r.1122g>t0.621
rrs1472973r.1128a>t0.621
rrs1472975r.1130t>a0.621
rrs1472977r.1132g>t0.667
rrs1472982r.1137g>c0.667
rrs1472987r.1142g>t0.667
rrs1472988r.1143t>a0.667
rrs1472989r.1144g>a0.667
rrs1472990r.1145a>t0.667
rrs1473002r.1157g>t0.821
rrs1473004r.1159t>a0.821
rrs1473008r.1163c>a0.821
rrs1473009r.1164t>c0.821
rrs1473053r.1208t>a0.939
rrs1473056r.1211a>t0.930
rrs1473062r.1217t>a0.946
rrs1473068r.1223a>g0.938
rrs1473081r.1236c>t0.942
rrs1473088r.1243a>g0.750
rrs1473130r.1285g>a0.902
rrs1473134r.1289t>c0.797
rrs1473141r.1296g>a0.893
rrs1473148r.1303g>a0.881
rrs1473158r.1313t>c0.899
rrs1473163r.1318c>t0.899
rrs1473177r.1332g>a0.903
rrs1473190r.1345g>t0.882
rrs1473192r.1347a>g0.882
rrs1473194r.1349a>g0.882
rrs1473205r.1360t>c0.900
rrs1473207r.1362c>a0.898
rrs1473248r.1403g>a0.917
rrs1473249r.1404t>c0.917
rrs1473252r.1407t>c0.917
rrs1473260r.1415g>t0.914
rrs1473261r.1416g>a0.914
rrs1473262r.1417t>c0.914
rrs1473276r.1431a>g0.877
rrs1473281r.1436c>g0.867
rrs1473288r.1443c>g0.846
rrs1473289r.1444t>c0.824
rrs1473290r.1445c>a0.824
rrs1473291r.1446g>a0.824
rrs1473297r.1452g>c0.830
rrs1473301r.1456t>c0.815
rrs1473305r.1460g>t0.815
rrs1473313r.1468g>t0.815
rrs1473314r.1469a>g0.815
rrs1473318r.1473g>a0.786
rrs1473319r.1474c>t0.786
rrs1473327r.1482a>g0.806
rrs1473328r.1483c>t0.792
rrs1473352r.1507c>t0.976
rrl1474218r.561t>a0.946
rrl1474228r.571t>c0.954
rrl1474249r.592g>t0.953
rrl1474252r.595t>a0.956
rrl1474263r.606g>a0.957
rrl1474269r.612c>t0.955
rrl1474277r.620c>a0.500
rrl1474557r.900g>a0.990
rrl1474558r.901g>t1.000
rrl1474570r.913g>t0.992
rrl1474578r.921a>g0.992
rrl1474582r.925t>c0.996
rrl1474584r.927c>g0.988
rrl1474586r.929t>a0.988
rrl1474758r.1101g>a0.243
rrl1474779r.1122g>t0.991
rrl1474780r.1123c>a0.991
rrl1474782r.1125g>a0.991
rrl1474790r.1133c>t0.991
rrl1474798r.1141c>t0.990
rrl1474799r.1142g>t0.990
rrl1474800r.1143t>g0.990
rrl1474801r.1144g>a0.991
rrl1474816r.1159g>c1.000
rrl1474823r.1166c>g1.000
rrl1474824r.1167a>g1.000
rrl1474825r.1168g>a1.000
rrl1474827r.1170c>t1.000
rrl1474831r.1174a>c1.000
rrl1474844r.1187g>t1.000
rrl1474864r.1207c>ct0.762
rrl1474866r.1209c>a1.000
rrl1474869r.1212g>c1.000
rrl1474896r.1239a>g1.000
rrl1474901r.1244a>g0.987
rrl1474903r.1246t>c0.987
rrl1474904r.1247g>c0.987
rrl1474910r.1253c>g0.987
rrl1474913r.1256t>a0.987
rrl1474920r.1263g>a0.987
rrl1475573r.1916g>gc1.000
rrl1475673r.2016t>c1.000
rrl1475688r.2031g>c1.000
rrl1475692r.2035g>t1.000
rrl1475707r.2050t>c1.000
rrl1475713r.2056c>g1.000
rrl1475716r.2059a>g1.000
rrl1475730r.2073g>a1.000
rrl1475745r.2088a>c1.000
rrl1475747r.2090a>g1.000
rrl1475751r.2094c>g1.000
rrl1475752r.2095c>a1.000
rrl1475753r.2096c>g1.000
rrl1475756r.2099t>c1.000
rrl1475760r.2103c>g1.000
rrl1475763r.2106c>g1.000
rrl1475766r.2109g>a1.000
rrl1475767r.2110g>c1.000
rrl1475769r.2112t>c1.000
rrl1475775r.2118g>t1.000
rrl1475776r.2119g>t1.000
rrl1475777r.2120a>c1.000
rrl1475781r.2124t>c1.000
rrl1475803r.2146t>c1.000
rrl1475804r.2147g>c1.000
rrl1475816r.2159c>g1.000
rrl1475817r.2160a>g1.000
rrl1476123r.2466g>c0.667
rrl1476128r.2471t>a0.714
rrl1476131r.2474c>t0.778
rrl1476135r.2478t>g0.889
rrl1476141r.2484a>g0.984
rrl1476153r.2496t>c0.985
rrl1476160r.2503t>c0.987
rrl1476165r.2508t>a0.987
rrl1476225r.2568t>g0.800
rrl1476229r.2572c>t0.929
rrl1476240r.2583g>a0.992
rrl1476251r.2594t>a0.992
rrl1476252r.2595t>a0.992
rrl1476260r.2603a>g0.992
rrl1476280r.2623a>c0.992
rrl1476293r.2636c>t0.938
rrl1476294r.2637a>g0.938
rrl1476295r.2638c>g0.937
rrl1476296r.2639c>t0.923
rrl1476297r.2640c>t0.908
rrl1476311r.2654g>c0.910
rrl1476312r.2655t>c0.910
rrl1476313r.2656g>a0.910
rrl1476332r.2675g>c0.936
rrl1476337r.2680c>t0.938
rrl1476353r.2696g>t0.947
rrl1476358r.2701t>c0.951
rrl1476382r.2725a>g0.928
rrl1476383r.2726t>a0.935
rrl1476425r.2768g>a0.942
rrl1476428r.2771c>t0.943
rrl1476443r.2786g>t0.944
rrl1476455r.2798c>a0.959
rrl1476466r.2809c>t0.968
rrl1476481r.2824t>c0.991
rrl1476506r.2849t>c0.994
rrl1476512r.2855c>t0.900
rrl1476547r.2890c>t0.995
rrl1476567r.2910c>t0.995
rrl1476573r.2916a>c0.993
rrl1476577r.2920t>g0.993
rrl1476580r.2923g>a0.993
rrl1476584r.2927c>t0.993
rrl1476585r.2928a>c0.993
rrl1476595r.2938c>a0.992
rrl1476602r.2945g>t0.961
rrl1476608r.2951c>g0.960
rrl1476619r.2962c>t0.737
katG2154724p.Arg463Leu1.000
katG2156142c.-31C>T0.200
kasA2519243p.Asp377Asn0.200
thyA3074389p.Ser28Ile0.235
ald3086788c.-32T>C1.000
gid4407980p.Pro75Ser0.200

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;