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: 5d7616a4189ae
Sample: 5d7616a4189ae

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Summary
ID: 5d7616a4189ae
Date: Mon Sep 9 10:11:34 2019
Strain: lineage1.1.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Trp (1.00)
EthambutolRembB p.Asp328Gly (1.00), embB p.Gly406Ser (1.00)
PyrazinamideRpncA Chromosome:g.2288682 2288768del (1.00)
StreptomycinRrpsL p.Lys43Arg (1.00), rrs r.888g>a (0.88)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1401a>g (0.36)
CapreomycinRrrs r.1401a>g (0.36)
KanamycinRrrs r.1401a>g (0.36)

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.Ser95Thr0.990
gyrA8452p.Ala384Val1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpoC763884p.Ala172Val1.000
rpoC763886c.517C>A1.000
rpoC764925p.Gly519Asp1.000
rpoC765171p.Pro601Leu1.000
rpoC765988c.2619G>A1.000
rpsL781395c.-165T>C1.000
embR1417019p.Cys110Tyr1.000
embR1417029p.Asp107Asn1.000
embR1417554c.-207C>G1.000
rrs1471878r.33c>t0.472
rrs1471896r.51t>c0.534
rrs1471900r.55c>t0.539
rrs1472101r.256g>a0.211
rrs1472102r.257g>a0.229
rrs1472112r.267c>t0.730
rrs1472122r.277g>a0.754
rrs1472127r.282c>t0.760
rrs1472128r.283g>a0.756
rrs1472129r.284g>c0.762
rrs1472137r.292g>a0.818
rrs1472150r.305t>a0.846
rrs1472151r.306c>t0.846
rrs1472164r.319g>a0.849
rrs1472172r.327t>c0.865
rrs1472177r.332c>t0.856
rrs1472203r.358g>a0.862
rrs1472210r.365a>c0.850
rrs1472213r.368g>c0.849
rrs1472215r.370a>g0.844
rrs1472225r.380c>a0.861
rrs1472234r.389t>c0.810
rrs1472236r.391c>g0.809
rrs1472240r.395g>a0.808
rrs1472251r.406g>a0.532
rrs1472253r.408g>t0.256
rrs1472344r.499c>t0.342
rrs1472378r.533g>t0.795
rrs1472379r.534t>g0.792
rrs1472382r.537g>a0.757
rrs1472389r.544g>a0.788
rrs1472400r.555c>t0.816
rrs1472412r.567a>c0.817
rrs1472415r.570t>g0.815
rrs1472422r.577t>c0.818
rrs1472507r.662c>g0.143
rrs1472517r.672t>a0.829
rrs1472518r.673g>t0.825
rrs1472530r.685g>a0.844
rrs1472541r.696t>g0.830
rrs1472544r.699c>a0.852
rrs1472545r.700a>t0.852
rrs1472557r.712g>a0.846
rrs1472570r.725g>a0.820
rrs1472571r.726g>c0.840
rrs1472573r.728c>t0.800
rrs1472579r.734g>t0.831
rrs1472581r.736a>t0.844
rrs1472596r.751g>t0.834
rrs1472598r.753a>t0.851
rrs1472614r.769g>t0.825
rrs1472616r.771g>a0.859
rrs1472655r.810g>a0.483
rrs1472658r.813g>a0.375
rrs1472661r.816a>g0.347
rrs1472665r.820g>a0.306
rrs1472678r.833t>c0.294
rrs1472679r.834t>c0.302
rrs1472690r.845c>a0.321
rrs1472695r.850c>t0.329
rrs1472697r.852t>c0.337
rrs1472713r.868t>c0.839
rrs1472716r.871c>t0.844
rrs1472742r.897c>t0.875
rrs1472744r.899a>g0.876
rrs1472767r.922g>a0.831
rrs1472781r.936c>t0.897
rrs1472793r.948a>t0.876
rrs1472803r.958t>a0.861
rrs1472824r.979t>a0.132
rrs1472895r.1050c>t0.837
rrs1473035r.1190g>a0.826
rrs1473053r.1208t>a0.211
rrs1473056r.1211a>t0.200
rrs1473062r.1217t>a0.200
rrs1473068r.1223a>g0.193
rrs1473145r.1300c>t0.765
rrs1473147r.1302g>t0.765
rrs1473148r.1303g>a0.762
rrs1473163r.1318c>t0.757
rrs1473164r.1319c>a0.757
rrs1473166r.1321g>a0.751
rrs1473172r.1327t>c0.745
rrs1473173r.1328c>t0.745
rrs1473177r.1332g>a0.753
rrs1473191r.1346c>t0.751
rrs1473202r.1357c>t0.719
rrs1473206r.1361g>a0.728
rrs1473226r.1381c>t0.767
rrs1473352r.1507c>t0.738
rrl1473679r.22t>c0.419
rrl1473697r.40c>a0.322
rrl1473792r.135c>t0.712
rrl1473797r.140g>t0.690
rrl1473803r.146g>a0.167
rrl1474218r.561t>a0.626
rrl1474236r.579g>a0.531
rrl1474252r.595t>a0.459
rrl1474255r.598c>t0.378
rrl1474269r.612c>t0.319
rrl1474330r.673a>t0.729
rrl1474338r.681g>a0.206
rrl1474341r.684t>g0.180
rrl1474387r.730c>t0.793
rrl1474777r.1120t>c0.182
rrl1474839r.1182c>t0.814
rrl1474844r.1187g>t0.816
rrl1474864r.1207c>t0.837
rrl1474866r.1209c>a0.833
rrl1474869r.1212g>t0.837
rrl1474892r.1235g>a0.767
rrl1474896r.1239a>g0.767
rrl1474902r.1245t>c0.756
rrl1474903r.1246t>a0.753
rrl1474904r.1247g>c0.753
rrl1474913r.1256t>a0.748
rrl1474920r.1263g>c0.743
rrl1475137r.1480a>t0.627
rrl1475144r.1487g>c0.624
rrl1475145r.1488c>t0.633
rrl1475163r.1506t>g0.698
rrl1475171r.1514c>t0.685
rrl1475175r.1518g>a0.696
rrl1475188r.1531c>t0.654
rrl1475498r.1841c>g0.158
rrl1475550r.1893a>c0.316
rrl1475552r.1895g>c0.520
rrl1475574r.1917c>a0.910
rrl1475713r.2056c>g0.905
rrl1475716r.2059a>g0.906
rrl1475783r.2126t>g0.342
rrl1475803r.2146t>c0.908
rrl1475804r.2147g>c0.907
rrl1475816r.2159c>g0.920
rrl1475817r.2160a>g0.920
rrl1475858r.2201t>c0.925
rrl1475866r.2209t>a0.910
rrl1476126r.2469c>t0.158
rrl1476130r.2473g>a0.154
rrl1476135r.2478t>c0.243
rrl1476141r.2484a>g0.835
rrl1476153r.2496t>c0.834
rrl1476165r.2508t>g0.829
rrl1476179r.2522c>t0.750
rrl1476194r.2537a>g0.200
rrl1476195r.2538c>a0.195
rrl1476196r.2539c>a0.195
rrl1476200r.2543a>t0.200
rrl1476201r.2544c>t0.205
rrl1476204r.2547c>a0.200
rrl1476210r.2553g>t0.190
rrl1476211r.2554g>t0.182
rrl1476212r.2555t>c0.178
rrl1476213r.2556g>a0.178
rrl1476214r.2557g>t0.174
rrl1476215r.2558c>a0.174
rrl1476225r.2568t>g0.851
rrl1476229r.2572c>t0.860
rrl1476260r.2603a>g0.848
rrl1476268r.2611a>t0.843
rrl1476275r.2618t>a0.832
rrl1476279r.2622g>a0.834
rrl1476280r.2623a>c0.831
rrl1476293r.2636c>t0.588
rrl1476294r.2637a>g0.588
rrl1476295r.2638c>g0.582
rrl1476296r.2639c>t0.582
rrl1476297r.2640c>t0.571
rrl1476301r.2644a>c0.576
rrl1476302r.2645g>a0.576
rrl1476311r.2654g>c0.586
rrl1476312r.2655t>c0.591
rrl1476313r.2656g>a0.593
rrl1476332r.2675g>c0.847
rrl1476353r.2696g>t0.868
rrl1476358r.2701t>c0.873
rrl1476369r.2712c>t0.872
rrl1476372r.2715t>c0.879
rrl1476382r.2725a>g0.879
rrl1476383r.2726t>a0.878
rrl1476408r.2751g>a0.860
rrl1476425r.2768g>t0.876
rrl1476428r.2771c>t0.870
rrl1476429r.2772a>c0.884
rrl1476466r.2809c>t0.888
rrl1476481r.2824t>c0.920
rrl1476506r.2849t>c0.897
rrl1476514r.2857c>t0.778
rrl1476517r.2860c>t0.770
rrl1476519r.2862c>g0.778
rrl1476524r.2867c>a0.762
rrl1476525r.2868a>g0.762
rrl1476530r.2873c>t0.755
rrl1476536r.2879g>a0.755
rrl1476537r.2880a>g0.755
rrl1476538r.2881a>g0.755
rrl1476540r.2883c>g0.762
rrl1476547r.2890c>t0.900
rrl1476567r.2910c>t0.902
rrl1476572r.2915g>a0.889
rrl1476573r.2916a>t0.886
rrl1476584r.2927c>t0.884
fabG11674048c.609G>A1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518132c.18C>T1.000
ahpC2726468c.276G>A1.000
thyX3067491p.Ala152Val1.000
ald3086788c.-32T>C1.000
ald3087219p.Ser134Gly1.000
fbiA3640446c.-97A>T1.000
alr3841652c.-232A>T0.266
alr3841654c.-234A>C0.271
alr3841662c.-242A>G0.344
alr3841663c.-243G>A0.318
embC4240671p.Thr270Ile1.000
embC4241042p.Asn394Asp1.000
embC4242643c.2781C>T1.000
embA4243848p.Val206Met1.000
embA4245969p.Pro913Ser1.000
embB4247646p.Glu378Ala1.000
ethA4326265p.Cys403Trp1.000
gid4407588c.615T>C1.000
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;