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: 5db4c7ac9539c
Sample: 5db4c7ac9539c

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Summary
ID: 5db4c7ac9539c
Date: Sat Oct 26 23:32:47 2019
Strain: lineage4.7
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.His445Asp (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.88), rrs r.1484g>t (0.87)
CapreomycinRrrs r.1402c>a (0.88), rrs r.1484g>t (0.87)
KanamycinRrrs r.1402c>a (0.88), rrs r.1484g>t (0.87)

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.7Euro-American (mainly T)T1;T5None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
rpoB762879p.Met1025Leu0.694
rpoB762899c.3093G>C0.786
rpoB762911c.3105C>T0.825
rpoB762917c.3111C>G0.825
rpoB762920c.3114C>T0.780
rpoB762923c.3117C>G0.786
rpoB762926c.3120C>G0.767
rpoB762929c.3123G>C0.739
rpoB762932c.3126G>C0.768
rpoB762959c.3153G>C0.827
rpoB762971c.3165G>C0.731
rpoB762989c.3183G>C0.690
rpoB762995c.3189G>T0.714
rpoC763528c.159G>A0.182
rpoC763531c.162G>C0.188
rpoC763532p.Thr55Ser0.188
rpoC763546c.177A>G0.718
rpoC763550p.Tyr61Ala0.718
rpoC763570c.201G>C0.786
rpoC763589p.Ile74Val0.815
rpoC763615c.246G>C0.174
rpoC763630c.261G>C0.229
rpoC763642c.273G>C0.750
rpoC763660c.291T>C0.773
rpoC763675c.306C>G0.752
rpoC763696c.327T>C0.784
rpoC763708c.339G>C0.761
rpoC763714c.345G>C0.676
rpoC763717c.348T>C0.677
rpoC763723c.354G>C0.596
rpoC763727p.Leu120Met0.628
rpoC763732c.363C>G0.590
rpoC763744c.375G>C0.514
rpoC763751p.Ile128Val0.227
rpoC764650c.1281G>T0.405
rpoC764653c.1284G>C0.385
rpoC764660p.Val431Ile0.375
rpoC764668c.1299C>A0.381
rpoC764671c.1302G>C0.364
rpoC764683c.1314G>C0.333
rpoC764706p.Leu446Gln0.349
rpoC764713c.1344G>C0.366
rpoC764716c.1347G>C0.357
rpsL781395c.-165T>C1.000
rrs1471853r.8t>c0.179
rrs1471878r.33c>t0.890
rrs1472067r.222g>c0.318
rrs1472075r.230a>g0.538
rrs1472078r.233c>t0.559
rrs1472102r.257g>a0.766
rrs1472106r.261g>a0.760
rrs1472108r.263c>t0.752
rrs1472112r.267c>t0.742
rrs1472113r.268t>c0.754
rrs1472123r.278a>t0.884
rrs1472150r.305t>a0.905
rrs1472172r.327t>c0.905
rrs1472225r.380c>a0.891
rrs1472240r.395g>a0.873
rrs1472251r.406g>a0.855
rrs1472284r.439c>t0.279
rrs1472328r.483g>c0.148
rrs1472333r.488g>a0.323
rrs1472338r.493a>g0.382
rrs1472344r.499c>t0.677
rrs1472379r.534t>c0.798
rrs1472382r.537g>a0.800
rrs1472389r.544g>a0.791
rrs1472400r.555c>t0.717
rrs1472422r.577t>c0.659
rrs1472494r.649a>g0.768
rrs1472496r.651t>g0.762
rrs1472498r.653c>t0.787
rrs1472507r.662c>t0.832
rrs1472558r.713g>a0.904
rrs1472569r.724g>a0.853
rrs1472571r.726g>a0.850
rrs1472581r.736a>c0.862
rrs1472606r.761c>g0.832
rrs1472616r.771g>a0.804
rrs1472623r.778a>c0.742
rrs1472645r.800g>c0.667
rrs1472655r.810g>t0.621
rrs1472660r.815t>a0.595
rrs1472666r.821g>t0.546
rrs1472694r.849c>a0.164
rrs1472697r.852t>c0.276
rrs1472714r.869a>t0.787
rrs1472767r.922g>a0.889
rrs1472790r.945t>c0.838
rrs1472824r.979t>a0.258
rrs1472825r.980g>a0.185
rrs1472828r.983t>c0.185
rrs1472895r.1050c>t0.894
rrs1472952r.1107t>c0.845
rrs1472955r.1110c>t0.736
rrs1472956r.1111t>c0.736
rrs1472957r.1112c>t0.842
rrs1472982r.1137g>a0.912
rrs1472987r.1142g>a0.904
rrs1472990r.1145a>g0.904
rrs1472993r.1148g>t0.905
rrs1473035r.1190g>a0.906
rrs1473055r.1210c>t0.876
rrs1473056r.1211a>t0.870
rrs1473066r.1221a>g0.841
rrs1473097r.1252g>a0.321
rrs1473100r.1255g>a0.280
rrs1473104r.1259c>t0.406
rrs1473110r.1265t>g0.459
rrs1473111r.1266a>g0.459
rrs1473121r.1276t>c0.711
rrs1473122r.1277t>a0.728
rrs1473134r.1289t>c0.858
rrs1473145r.1300c>t0.871
rrs1473147r.1302g>a0.869
rrs1473164r.1319c>t0.894
rrs1473166r.1321g>a0.902
rrs1473226r.1381c>t0.897
rrs1473269r.1424c>t0.804
rrs1473276r.1431a>g0.820
rrs1473283r.1438t>c0.826
rrs1473290r.1445c>t0.816
rrs1473301r.1456t>c0.885
rrs1473319r.1474c>t0.851
rrs1473320r.1475g>a0.864
rrs1473324r.1479g>a0.856
rrl1474155r.498g>a0.241
rrl1474164r.507c>t0.733
rrl1474166r.509g>a0.736
rrl1474183r.526t>c0.854
rrl1474184r.527c>a0.854
rrl1474201r.544t>c0.882
rrl1474202r.545t>a0.883
rrl1474218r.561t>a0.904
rrl1474249r.592g>t0.878
rrl1474265r.608g>t0.812
rrl1474269r.612c>t0.795
rrl1474275r.618t>a0.793
rrl1474280r.623c>t0.784
rrl1474281r.624a>g0.772
rrl1474292r.635t>a0.185
rrl1474316r.659t>c0.314
rrl1474317r.660g>a0.342
rrl1474348r.691c>t0.779
rrl1474351r.694g>c0.779
rrl1474354r.697c>t0.779
rrl1474356r.699t>c0.777
rrl1474359r.702c>g0.771
rrl1474362r.705a>g0.771
rrl1474387r.730c>t0.786
rrl1474454r.797g>a0.263
rrl1474466r.809g>a0.881
rrl1474476r.819c>t0.927
rrl1474488r.831g>t0.937
rrl1474496r.839c>a0.939
rrl1474497r.840g>c0.942
rrl1474506r.849c>g0.950
rrl1474507r.850g>t0.951
rrl1474516r.859c>a0.956
rrl1474537r.880g>a0.955
rrl1474558r.901g>a0.953
rrl1474583r.926c>t0.952
rrl1474601r.944c>t0.946
rrl1474632r.975g>t0.902
rrl1474636r.979a>t0.899
rrl1474637r.980c>t0.904
rrl1474638r.981c>g0.904
rrl1474639r.982g>c0.899
rrl1474676r.1019t>a0.912
rrl1474783r.1126g>a0.185
rrl1474790r.1133c>t0.826
rrl1474794r.1137c>t0.860
rrl1474800r.1143t>c0.866
rrl1474823r.1166c>g0.921
rrl1474827r.1170c>t0.917
rrl1474830r.1173a>t0.912
rrl1474831r.1174a>t0.912
rrl1474832r.1175a>t0.915
rrl1474904r.1247g>c0.815
rrl1474905r.1248t>c0.810
rrl1474913r.1256t>c0.800
rrl1474920r.1263g>a0.755
rrl1474935r.1278a>g0.304
rrl1474938r.1281g>a0.190
rrl1475084r.1427g>t0.385
rrl1475104r.1447t>a0.630
rrl1475108r.1451c>t0.644
rrl1475111r.1454g>a0.636
rrl1475114r.1457c>t0.659
rrl1475116r.1459g>a0.644
rrl1475119r.1462c>t0.674
rrl1475120r.1463g>t0.674
rrl1475124r.1467a>t0.741
rrl1475129r.1472g>a0.781
rrl1475508r.1851a>t0.768
rrl1475526r.1869c>a0.716
rrl1475536r.1879c>a0.739
rrl1475538r.1881t>a0.731
rrl1475539r.1882a>t0.731
rrl1475545r.1888t>g0.723
rrl1475548r.1891c>t0.723
rrl1475549r.1892t>c0.723
rrl1475550r.1893a>g0.723
rrl1475599r.1942a>g0.344
rrl1475657r.2000a>g0.194
rrl1475659r.2002g>t0.188
rrl1475692r.2035g>c0.895
rrl1475753r.2096c>g0.916
rrl1475759r.2102c>g0.902
rrl1475769r.2112t>c0.918
rrl1475775r.2118g>t0.931
rrl1475881r.2224t>c0.922
rrl1475896r.2239a>g0.870
rrl1475897r.2240t>c0.874
rrl1475898r.2241a>g0.868
rrl1475899r.2242g>a0.876
rrl1475916r.2259c>t0.910
rrl1475943r.2286g>a0.913
rrl1475952r.2295a>g0.910
rrl1475963r.2306g>t0.915
rrl1475970r.2313c>t0.903
rrl1475977r.2320a>g0.892
rrl1475988r.2331a>g0.800
rrl1475997r.2340a>g0.464
rrl1475998r.2341c>t0.444
rrl1476001r.2344t>c0.423
rrl1476110r.2453g>c0.143
rrl1476115r.2458t>c0.627
rrl1476131r.2474c>t0.903
rrl1476160r.2503t>c0.924
rrl1476200r.2543a>t0.927
rrl1476201r.2544c>t0.928
rrl1476224r.2567a>g0.892
rrl1476245r.2588c>t0.841
rrl1476252r.2595t>g0.822
rrl1476256r.2599a>g0.811
rrl1476260r.2603a>g0.805
rrl1476281r.2624t>c0.746
rrl1476309r.2652g>c0.347
rrl1476311r.2654g>c0.400
rrl1476337r.2680c>t0.884
rrl1476359r.2702c>g0.912
rrl1476381r.2724g>c0.921
rrl1476428r.2771c>t0.926
rrl1476466r.2809c>t0.906
rrl1476506r.2849t>c0.872
rrl1476515r.2858c>t0.824
rrl1476524r.2867c>a0.355
tlyA1917972c.33A>G1.000
embC4242643c.2781C>T1.000
embB4249732c.3219C>G1.000
gid4407590p.Ala205Thr1.000

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;