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: 5d1988745dd50
Sample: 5d1988745dd50

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Summary
ID: 5d1988745dd50
Date: Mon Jul 1 05:15:53 2019
Strain: lineage4.3.4.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00)
EthambutolRembB p.Met306Ile (1.00)
PyrazinamideRpncA p.Leu116Pro (1.00)
StreptomycinRrpsL p.Lys88Thr (1.00), rrs r.888g>a (0.82)
EthionamideRethA c.203 204insT (0.92)
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

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB761455p.Glu550Gly1.000
rpoC764995c.1626C>G1.000
rpsL781395c.-165T>C1.000
rrs1471878r.33c>t0.828
rrs1471896r.51t>c0.794
rrs1471900r.55c>t0.800
rrs1471948r.103a>g0.238
rrs1472101r.256g>a0.153
rrs1472102r.257g>a0.153
rrs1472106r.261g>a0.389
rrs1472112r.267c>t0.764
rrs1472127r.282c>t0.775
rrs1472128r.283g>a0.772
rrs1472129r.284g>c0.775
rrs1472137r.292g>a0.783
rrs1472150r.305t>a0.817
rrs1472151r.306c>t0.817
rrs1472164r.319g>a0.835
rrs1472172r.327t>c0.858
rrs1472177r.332c>t0.858
rrs1472203r.358g>a0.884
rrs1472210r.365a>c0.821
rrs1472213r.368g>c0.818
rrs1472215r.370a>g0.825
rrs1472225r.380c>a0.810
rrs1472234r.389t>c0.776
rrs1472236r.391c>g0.762
rrs1472240r.395g>a0.763
rrs1472251r.406g>a0.226
rrs1472344r.499c>t0.476
rrs1472378r.533g>t0.833
rrs1472379r.534t>g0.840
rrs1472382r.537g>a0.841
rrs1472389r.544g>a0.843
rrs1472400r.555c>t0.829
rrs1472412r.567a>c0.813
rrs1472415r.570t>g0.800
rrs1472422r.577t>c0.808
rrs1472517r.672t>a0.711
rrs1472518r.673g>t0.712
rrs1472530r.685g>a0.720
rrs1472541r.696t>g0.723
rrs1472544r.699c>a0.724
rrs1472545r.700a>t0.725
rrs1472557r.712g>a0.746
rrs1472570r.725g>a0.733
rrs1472571r.726g>c0.730
rrs1472573r.728c>t0.742
rrs1472579r.734g>t0.769
rrs1472581r.736a>t0.779
rrs1472596r.751g>t0.822
rrs1472598r.753a>t0.831
rrs1472614r.769g>t0.826
rrs1472616r.771g>a0.825
rrs1472655r.810g>a0.486
rrs1472658r.813g>a0.438
rrs1472661r.816a>g0.397
rrs1472665r.820g>a0.386
rrs1472678r.833t>c0.400
rrs1472679r.834t>c0.391
rrs1472690r.845c>a0.365
rrs1472695r.850c>t0.480
rrs1472697r.852t>c0.495
rrs1472713r.868t>c0.807
rrs1472716r.871c>t0.818
rrs1472742r.897c>t0.828
rrs1472744r.899a>g0.829
rrs1472767r.922g>a0.838
rrs1472781r.936c>t0.842
rrs1472793r.948a>t0.818
rrs1472803r.958t>a0.793
rrs1472880r.1035g>ga0.305
rrs1472895r.1050c>t0.772
rrs1473009r.1164t>c0.149
rrs1473035r.1190g>a0.851
rrs1473053r.1208t>a0.333
rrs1473054r.1209c>t0.254
rrs1473055r.1210c>t0.259
rrs1473056r.1211a>t0.254
rrs1473062r.1217t>a0.237
rrs1473068r.1223a>g0.246
rrs1473080r.1235c>a0.241
rrs1473082r.1237g>a0.241
rrs1473083r.1238g>a0.220
rrs1473094r.1249t>a0.200
rrs1473097r.1252g>t0.200
rrs1473099r.1254t>a0.200
rrs1473100r.1255g>a0.200
rrs1473110r.1265t>c0.190
rrs1473112r.1267a>t0.190
rrs1473115r.1270g>a0.193
rrs1473121r.1276t>c0.186
rrs1473122r.1277t>a0.186
rrs1473123r.1278a>t0.186
rrs1473128r.1283c>t0.183
rrs1473129r.1284c>t0.190
rrs1473131r.1286g>t0.300
rrs1473145r.1300c>t0.809
rrs1473147r.1302g>t0.812
rrs1473148r.1303g>a0.812
rrs1473163r.1318c>t0.816
rrs1473164r.1319c>a0.827
rrs1473166r.1321g>a0.816
rrs1473172r.1327t>c0.826
rrs1473173r.1328c>t0.833
rrs1473177r.1332g>a0.833
rrs1473191r.1346c>t0.839
rrs1473202r.1357c>t0.849
rrs1473206r.1361g>a0.853
rrs1473226r.1381c>t0.868
rrs1473248r.1403g>a0.500
rrs1473249r.1404t>c0.477
rrs1473252r.1407t>c0.467
rrs1473255r.1410a>g0.447
rrs1473259r.1414c>t0.467
rrs1473260r.1415g>t0.457
rrs1473276r.1431a>g0.326
rrs1473281r.1436c>a0.214
rrs1473282r.1437c>g0.214
rrs1473288r.1443c>t0.225
rrs1473290r.1445c>a0.237
rrs1473291r.1446g>t0.237
rrs1473296r.1451g>c0.265
rrs1473297r.1452g>t0.265
rrs1473301r.1456t>c0.250
rrs1473327r.1482a>g0.316
rrs1473328r.1483c>t0.316
rrs1473352r.1507c>t0.916
rrl1473679r.22t>c0.333
rrl1473788r.131a>g0.278
rrl1473797r.140g>t0.824
rrl1474218r.561t>a0.370
rrl1474236r.579g>a0.385
rrl1474249r.592g>t0.224
rrl1474252r.595t>a0.241
rrl1474255r.598c>t0.224
rrl1474269r.612c>t0.212
rrl1474330r.673a>t0.819
rrl1474338r.681g>a0.333
rrl1474387r.730c>t0.861
rrl1474777r.1120t>c0.422
rrl1474779r.1122g>a0.222
rrl1474782r.1125g>a0.222
rrl1474839r.1182c>t0.854
rrl1474844r.1187g>t0.863
rrl1474864r.1207c>t0.860
rrl1474866r.1209c>a0.839
rrl1474869r.1212g>t0.839
rrl1474892r.1235g>a0.779
rrl1474896r.1239a>g0.775
rrl1474902r.1245t>c0.768
rrl1474903r.1246t>a0.773
rrl1474904r.1247g>c0.773
rrl1474913r.1256t>a0.767
rrl1474920r.1263g>c0.768
rrl1475137r.1480a>t0.351
rrl1475144r.1487g>c0.361
rrl1475145r.1488c>t0.361
rrl1475154r.1497c>t0.423
rrl1475163r.1506t>g0.429
rrl1475171r.1514c>t0.418
rrl1475175r.1518g>a0.453
rrl1475188r.1531c>t0.403
rrl1475552r.1895g>c0.384
rrl1475574r.1917c>a0.848
rrl1475713r.2056c>g0.830
rrl1475716r.2059a>g0.841
rrl1475803r.2146t>c0.865
rrl1475804r.2147g>c0.869
rrl1475816r.2159c>g0.889
rrl1475817r.2160a>g0.889
rrl1475858r.2201t>c0.915
rrl1475866r.2209t>a0.909
rrl1476141r.2484a>g0.383
rrl1476153r.2496t>c0.360
rrl1476164r.2507a>g0.400
rrl1476165r.2508t>a0.400
rrl1476179r.2522c>t0.296
rrl1476188r.2531c>t0.264
rrl1476225r.2568t>g0.838
rrl1476229r.2572c>t0.836
rrl1476234r.2577g>a0.850
rrl1476260r.2603a>g0.847
rrl1476268r.2611a>t0.836
rrl1476275r.2618t>a0.813
rrl1476279r.2622g>a0.813
rrl1476280r.2623a>c0.817
rrl1476293r.2636c>t0.710
rrl1476294r.2637a>g0.705
rrl1476295r.2638c>g0.699
rrl1476296r.2639c>t0.699
rrl1476297r.2640c>t0.705
rrl1476301r.2644a>c0.691
rrl1476302r.2645g>a0.699
rrl1476311r.2654g>c0.731
rrl1476312r.2655t>c0.744
rrl1476313r.2656g>a0.748
rrl1476332r.2675g>c0.891
rrl1476353r.2696g>t0.911
rrl1476358r.2701t>c0.906
rrl1476369r.2712c>t0.906
rrl1476372r.2715t>c0.905
rrl1476382r.2725a>g0.909
rrl1476383r.2726t>a0.915
rrl1476408r.2751g>a0.915
rrl1476425r.2768g>t0.876
rrl1476428r.2771c>t0.873
rrl1476429r.2772a>c0.873
rrl1476466r.2809c>t0.911
rrl1476481r.2824t>c0.908
rrl1476506r.2849t>c0.856
rrl1476514r.2857c>t0.729
rrl1476517r.2860c>t0.706
rrl1476519r.2862c>g0.704
rrl1476524r.2867c>a0.713
rrl1476525r.2868a>g0.706
rrl1476530r.2873c>t0.706
rrl1476536r.2879g>a0.706
rrl1476537r.2880a>g0.713
rrl1476538r.2881a>g0.681
rrl1476540r.2883c>g0.684
rrl1476547r.2890c>t0.859
rrl1476567r.2910c>t0.850
rrl1476572r.2915g>a0.837
rrl1476573r.2916a>t0.837
rrl1476584r.2927c>t0.818
tlyA1917972c.33A>G1.000
folC2747453p.Arg49Gln1.000
thyA3073868p.Thr202Ala0.981
thyA3074361c.111A>G1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
embB4248736c.2223G>T1.000
gid4408054p.Leu50Arg1.000
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;