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: 5d7627d12a66f
Sample: 5d7627d12a66f

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Summary
ID: 5d7627d12a66f
Date: Mon Sep 9 11:25:33 2019
Strain: lineage1.1.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRfabG1 c.-15C>T (1.00), inhA p.Ile21Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00)
EthambutolRembB p.Gly406Ser (1.00)
PyrazinamideRpncA c.461 462insC (0.96)
StreptomycinRrrs r.888g>a (0.87)
EthionamideRfabG1 c.-15C>T (1.00), inhA p.Ile21Thr (1.00)
Fluoroquinolones
AmikacinRrrs r.1401a>g (0.22)
CapreomycinRrrs r.1401a>g (0.22)
KanamycinRrrs r.1401a>g (0.22)

Lineage2FamilyMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6112p.Met291Ile1.000
gyrB6124c.885C>T1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8452p.Ala384Val1.000
gyrA9047c.1746C>T1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
gyrA9443c.2142G>A1.000
rpoB759546c.-261A>G1.000
rpoB760490c.684C>T1.000
rpoB763031c.3225T>C1.000
rpoC763884p.Ala172Val1.000
rpoC763886c.517C>A1.000
rpoC765171p.Pro601Leu1.000
rpoC765461p.Asn698His1.000
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.146
embR1416234p.Cys372Gly0.147
embR1417019p.Cys110Tyr1.000
embR1417554c.-207C>G1.000
rrs1471850r.5g>t0.394
rrs1471852r.7t>a0.361
rrs1471878r.33c>t0.829
rrs1471896r.51t>c0.823
rrs1471900r.55c>t0.823
rrs1471948r.103a>g0.293
rrs1472101r.256g>a0.469
rrs1472102r.257g>a0.469
rrs1472106r.261g>a0.649
rrs1472112r.267c>t0.806
rrs1472122r.277g>a0.676
rrs1472127r.282c>t0.818
rrs1472129r.284g>c0.828
rrs1472137r.292g>a0.832
rrs1472150r.305t>a0.848
rrs1472151r.306c>t0.836
rrs1472164r.319g>a0.844
rrs1472172r.327t>c0.852
rrs1472177r.332c>t0.847
rrs1472203r.358g>a0.865
rrs1472210r.365a>c0.826
rrs1472213r.368g>c0.822
rrs1472215r.370a>g0.829
rrs1472225r.380c>a0.856
rrs1472234r.389t>c0.801
rrs1472236r.391c>g0.791
rrs1472240r.395g>a0.779
rrs1472251r.406g>a0.519
rrs1472253r.408g>t0.136
rrs1472344r.499c>t0.547
rrs1472378r.533g>t0.849
rrs1472379r.534t>g0.848
rrs1472382r.537g>a0.848
rrs1472389r.544g>a0.869
rrs1472400r.555c>t0.867
rrs1472412r.567a>c0.850
rrs1472415r.570t>g0.847
rrs1472422r.577t>c0.848
rrs1472507r.662c>g0.250
rrs1472517r.672t>a0.827
rrs1472518r.673g>t0.827
rrs1472530r.685g>a0.837
rrs1472541r.696t>g0.834
rrs1472544r.699c>a0.843
rrs1472545r.700a>t0.844
rrs1472557r.712g>a0.872
rrs1472570r.725g>a0.843
rrs1472571r.726g>c0.843
rrs1472573r.728c>t0.843
rrs1472579r.734g>t0.844
rrs1472581r.736a>t0.849
rrs1472596r.751g>t0.829
rrs1472598r.753a>t0.838
rrs1472614r.769g>t0.856
rrs1472616r.771g>a0.847
rrs1472655r.810g>a0.707
rrs1472658r.813g>a0.671
rrs1472661r.816a>g0.635
rrs1472665r.820g>a0.644
rrs1472678r.833t>c0.603
rrs1472679r.834t>c0.588
rrs1472690r.845c>a0.580
rrs1472695r.850c>t0.644
rrs1472697r.852t>c0.681
rrs1472713r.868t>c0.847
rrs1472716r.871c>t0.848
rrs1472742r.897c>t0.871
rrs1472744r.899a>g0.871
rrs1472767r.922g>a0.884
rrs1472781r.936c>t0.877
rrs1472793r.948a>t0.885
rrs1472803r.958t>a0.907
rrs1472880r.1035g>ga0.443
rrs1472895r.1050c>t0.892
rrs1473008r.1163ct>c0.190
rrs1473009r.1164t>c0.171
rrs1473035r.1190g>a0.903
rrs1473053r.1208t>a0.383
rrs1473054r.1209c>t0.383
rrs1473055r.1210c>t0.404
rrs1473056r.1211a>t0.404
rrs1473062r.1217t>a0.358
rrs1473068r.1223a>g0.345
rrs1473080r.1235c>a0.333
rrs1473082r.1237g>a0.321
rrs1473083r.1238g>a0.328
rrs1473094r.1249t>a0.281
rrs1473099r.1254t>a0.233
rrs1473100r.1255g>a0.242
rrs1473110r.1265t>c0.237
rrs1473115r.1270g>a0.217
rrs1473145r.1300c>t0.131
rrs1473147r.1302g>t0.129
rrs1473148r.1303g>a0.129
rrs1473177r.1332g>a0.277
rrs1473191r.1346c>t0.770
rrs1473202r.1357c>t0.768
rrs1473206r.1361g>a0.771
rrs1473226r.1381c>t0.796
rrs1473248r.1403g>a0.200
rrs1473249r.1404t>c0.208
rrs1473252r.1407t>c0.216
rrs1473255r.1410a>g0.216
rrs1473259r.1414c>t0.224
rrs1473260r.1415g>t0.220
rrs1473327r.1482a>g0.157
rrs1473328r.1483c>t0.173
rrs1473352r.1507c>t0.845
rrl1473782r.125a>g0.128
rrl1473797r.140g>t0.128
rrl1474218r.561t>a0.832
rrl1474236r.579g>a0.803
rrl1474252r.595t>a0.748
rrl1474255r.598c>t0.748
rrl1474269r.612c>t0.661
rrl1474330r.673a>t0.810
rrl1474338r.681g>a0.355
rrl1474341r.684t>g0.273
rrl1474348r.691c>t0.172
rrl1474381r.724t>g0.175
rrl1474777r.1120t>c0.270
rrl1474779r.1122g>a0.203
rrl1474782r.1125g>a0.206
rrl1474839r.1182c>t0.773
rrl1474844r.1187g>t0.778
rrl1474864r.1207c>t0.799
rrl1474866r.1209c>a0.799
rrl1474869r.1212g>t0.805
rrl1474892r.1235g>a0.746
rrl1474896r.1239a>g0.750
rrl1474902r.1245t>c0.744
rrl1474903r.1246t>a0.744
rrl1474904r.1247g>c0.748
rrl1474913r.1256t>a0.744
rrl1474920r.1263g>c0.738
rrl1475137r.1480a>t0.777
rrl1475144r.1487g>c0.788
rrl1475145r.1488c>t0.791
rrl1475163r.1506t>g0.792
rrl1475171r.1514c>t0.778
rrl1475175r.1518g>a0.778
rrl1475188r.1531c>t0.724
rrl1475498r.1841c>g0.750
rrl1475550r.1893a>c0.306
rrl1475552r.1895g>c0.566
rrl1475574r.1917c>a0.864
rrl1475713r.2056c>g0.862
rrl1475716r.2059a>g0.859
rrl1475782r.2125t>c0.211
rrl1475783r.2126t>g0.250
rrl1475803r.2146t>c0.907
rrl1475804r.2147g>c0.907
rrl1475816r.2159c>g0.915
rrl1475817r.2160a>g0.915
rrl1475858r.2201t>c0.955
rrl1475866r.2209t>a0.930
rrl1475877r.2220c>t0.211
rrl1476135r.2478t>c0.831
rrl1476141r.2484a>g0.832
rrl1476153r.2496t>c0.823
rrl1476165r.2508t>g0.812
rrl1476179r.2522c>t0.800
rrl1476225r.2568t>g0.819
rrl1476229r.2572c>t0.821
rrl1476251r.2594t>c0.844
rrl1476260r.2603a>g0.825
rrl1476268r.2611a>t0.812
rrl1476275r.2618t>a0.798
rrl1476279r.2622g>a0.787
rrl1476280r.2623a>c0.787
rrl1476293r.2636c>t0.538
rrl1476294r.2637a>g0.538
rrl1476295r.2638c>g0.538
rrl1476296r.2639c>t0.544
rrl1476297r.2640c>t0.544
rrl1476301r.2644a>c0.538
rrl1476302r.2645g>a0.538
rrl1476311r.2654g>c0.594
rrl1476312r.2655t>c0.594
rrl1476313r.2656g>a0.606
rrl1476332r.2675g>c0.844
rrl1476353r.2696g>t0.887
rrl1476358r.2701t>c0.883
rrl1476369r.2712c>t0.875
rrl1476372r.2715t>c0.880
rrl1476382r.2725a>g0.877
rrl1476383r.2726t>a0.881
rrl1476408r.2751g>a0.892
rrl1476425r.2768g>t0.896
rrl1476428r.2771c>t0.895
rrl1476429r.2772a>c0.903
rrl1476466r.2809c>t0.912
rrl1476481r.2824t>c0.913
rrl1476506r.2849t>c0.866
rrl1476514r.2857c>t0.732
rrl1476517r.2860c>t0.705
rrl1476519r.2862c>g0.705
rrl1476524r.2867c>a0.683
rrl1476525r.2868a>g0.683
rrl1476530r.2873c>t0.694
rrl1476536r.2879g>a0.699
rrl1476537r.2880a>g0.699
rrl1476538r.2881a>g0.694
rrl1476540r.2883c>g0.707
rrl1476547r.2890c>t0.843
rrl1476567r.2910c>t0.826
rrl1476572r.2915g>a0.814
rrl1476573r.2916a>t0.808
rrl1476584r.2927c>t0.800
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518132c.18C>T1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.209
alr3841654c.-234A>C0.202
alr3841662c.-242A>G0.293
alr3841663c.-243G>A0.258
embC4240671p.Thr270Ile1.000
embC4241042p.Asn394Asp1.000
embC4242643c.2781C>T1.000
embA4243848p.Val206Met1.000
embA4245969p.Pro913Ser1.000
embB4246584p.Arg24Pro0.275
embB4247646p.Glu378Ala1.000
embB4248412c.1899C>T1.000
ethA4326899p.Pro192Leu1.000
gid4407588c.615T>C1.000
gid4407598p.Val202Gly1.000
gid4407873c.330C>A1.000

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;