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: 5cc5421158561
Sample: 5cc5421158561

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Summary
ID: 5cc5421158561
Date: Sun Apr 28 07:04:18 2019
Strain: lineageBOV;lineage4.3;lineage4.3.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineageBOVM. bovisBOV 1;BOV 2None
lineage4.3.1Euro-American (LAM)LAM9None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rpoB760199c.393C>G1.000
rpoB760235c.429T>C1.000
rpoB762929c.3123G>C1.000
rpoB762962c.3156C>T1.000
rpoB762995c.3189G>T1.000
rpoB763050c.3244C>T1.000
rpoB763053c.3247T>C1.000
rpoB763058c.3252C>G0.917
rpoB763070c.3264T>C1.000
rpoB763094c.3288G>C1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763136c.3330C>T1.000
rpoB763142c.3336C>G1.000
rpoB763169c.3363A>G1.000
rpoB763227c.3421C>T1.000
rpoB763238c.3432T>C1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763657c.288G>A1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>T1.000
rpoC763669c.300C>G1.000
rpoC764713c.1344G>A1.000
rpoC764716c.1347G>C1.000
rpoC765628c.2259G>C1.000
rpoC765662c.2293T>C1.000
rpoC765673p.Asp768Glu1.000
rrs1471852r.7t>a0.455
rrs1471896r.51t>c0.837
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471936r.91a>g1.000
rrs1471985r.140t>c1.000
rrs1471986r.141c>t1.000
rrs1471996r.151c>t1.000
rrs1472029r.184c>t1.000
rrs1472041r.196c>t1.000
rrs1472042r.197t>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t1.000
rrs1472127r.282c>t0.481
rrs1472128r.283g>c0.481
rrs1472129r.284g>a0.370
rrs1472138r.293c>t0.485
rrs1472147r.302g>a0.500
rrs1472150r.305t>a0.500
rrs1472151r.306c>a0.500
rrs1472172r.327t>c0.622
rrs1472210r.365a>c0.150
rrs1472327r.482g>a1.000
rrs1472328r.483g>c1.000
rrs1472344r.499c>t0.261
rrs1472378r.533g>t0.630
rrs1472379r.534t>g0.686
rrs1472400r.555c>t0.688
rrs1472415r.570t>g0.568
rrs1472422r.577t>c0.150
rrs1472438r.593t>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472456r.611t>c1.000
rrs1472464r.619a>g1.000
rrs1472489r.644a>g1.000
rrs1472498r.653c>t0.955
rrs1472683r.838t>tta0.923
rrs1472700r.855c>t0.205
rrs1472708r.863t>a0.628
rrs1472742r.897c>t0.757
rrs1472744r.899a>g0.759
rrs1472781r.936c>t0.764
rrs1472786r.941c>t0.765
rrs1472793r.948a>t0.776
rrs1472803r.958t>c0.733
rrs1472824r.979t>a0.303
rrs1472847r.1002g>c1.000
rrs1472848r.1003t>g1.000
rrs1472849r.1004c>g1.000
rrs1472858r.1013g>t1.000
rrs1472859r.1014g>c1.000
rrs1472860r.1015c>g1.000
rrs1472953r.1108g>a0.596
rrs1472956r.1111t>c0.583
rrs1472957r.1112c>t0.590
rrs1472969r.1124a>g0.225
rrs1472970r.1125c>a0.244
rrs1472973r.1128a>t0.763
rrs1472975r.1130t>a0.205
rrs1472977r.1132g>t0.190
rrs1472978r.1133t>c0.195
rrs1472982r.1137g>a0.195
rrs1472987r.1142g>a0.195
rrs1472990r.1145a>g0.200
rrs1473001r.1156g>c0.205
rrs1473002r.1157g>a0.205
rrs1473004r.1159t>a0.205
rrs1473008r.1163c>t0.205
rrs1473009r.1164t>g0.200
rrs1473020r.1175t>c0.190
rrs1473100r.1255g>c1.000
rrs1473104r.1259c>t1.000
rrs1473109r.1264t>g0.944
rrs1473111r.1266a>t1.000
rrs1473123r.1278a>t1.000
rrs1473145r.1300c>t0.140
rrs1473147r.1302g>c0.524
rrs1473148r.1303g>a0.524
rrs1473150r.1305t>g0.568
rrs1473161r.1316a>c0.481
rrs1473163r.1318c>t0.473
rrs1473164r.1319c>g0.508
rrs1473166r.1321g>a0.423
rrs1473177r.1332g>a0.611
rrs1473199r.1354ca>c0.623
rrs1473202r.1357c>t0.613
rrs1473248r.1403g>a0.350
rrs1473249r.1404t>c0.350
rrs1473252r.1407t>c0.350
rrs1473259r.1414c>t0.368
rrs1473262r.1417t>a0.395
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473301r.1456t>c1.000
rrs1473352r.1507c>t0.526
rrl1473384c.-274A>G0.423
rrl1473770r.113t>g1.000
rrl1474083r.426c>t0.905
rrl1474089r.432c>t0.900
rrl1474093r.436g>a1.000
rrl1474103r.446a>t1.000
rrl1474105r.448t>g0.895
rrl1474108r.451c>g0.895
rrl1474110r.453a>t0.950
rrl1474116r.459g>a0.952
rrl1474127r.470g>a0.950
rrl1474139r.482c>t0.952
rrl1474151r.494c>t1.000
rrl1474174r.517a>g0.950
rrl1474181r.524c>t1.000
rrl1474201r.544t>c1.000
rrl1474202r.545t>g0.938
rrl1474249r.592g>t0.941
rrl1474263r.606g>a0.933
rrl1474350r.693g>c1.000
rrl1474351r.694g>c1.000
rrl1474353r.696a>g1.000
rrl1474356r.699t>c1.000
rrl1474362r.705a>g1.000
rrl1474374r.717t>g0.941
rrl1474412r.755g>gt0.364
rrl1474452r.795c>g1.000
rrl1474552r.895c>t1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t1.000
rrl1474638r.981c>a1.000
rrl1474639r.982g>c1.000
rrl1474715r.1058ta>t1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1475031r.1374g>t1.000
rrl1475037r.1380t>c1.000
rrl1475061r.1404c>t1.000
rrl1475062r.1405a>g1.000
rrl1475120r.1463g>t1.000
rrl1475206r.1549c>t1.000
rrl1475209r.1552g>c1.000
rrl1475213r.1556c>t1.000
rrl1475291r.1634a>c1.000
rrl1475297r.1640c>t1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475363r.1706c>t1.000
rrl1475452r.1795c>a1.000
rrl1475458r.1801c>t1.000
rrl1475460r.1803a>g1.000
rrl1475482r.1825a>g1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475544r.1887a>t1.000
rrl1475545r.1888t>g1.000
rrl1475573r.1916g>a1.000
rrl1475659r.2002g>a1.000
rrl1475753r.2096c>g1.000
rrl1475762r.2105g>t1.000
rrl1475763r.2106c>t1.000
rrl1475764r.2107a>c1.000
rrl1475765r.2108a>g1.000
rrl1475775r.2118g>t1.000
rrl1475783r.2126t>g0.640
rrl1475803r.2146t>c0.623
rrl1475804r.2147g>c0.607
rrl1475816r.2159c>g0.617
rrl1475817r.2160a>g0.627
rrl1475858r.2201t>c0.609
rrl1475866r.2209t>a0.571
rrl1475869r.2212c>t0.550
rrl1475916r.2259c>t1.000
rrl1475975r.2318c>t0.944
rrl1475977r.2320a>g0.941
rrl1475995r.2338g>a0.917
rrl1475997r.2340a>g0.923
rrl1476033r.2376t>c1.000
rrl1476034r.2377c>g1.000
rrl1476035r.2378g>c1.000
rrl1476044r.2387t>g1.000
rrl1476045r.2388g>t1.000
rrl1476049r.2392c>t1.000
rrl1476086r.2429g>a1.000
rrl1476088r.2431a>c1.000
rrl1476095r.2438c>t1.000
rrl1476103r.2446c>a1.000
rrl1476108r.2451t>g1.000
rrl1476110r.2453g>t1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476214r.2557g>t0.933
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g0.700
rrl1476225r.2568t>g0.316
rrl1476229r.2572c>g0.304
rrl1476245r.2588c>t0.545
rrl1476246r.2589g>a0.545
rrl1476251r.2594t>g0.455
rrl1476252r.2595t>g0.545
rrl1476256r.2599a>g0.455
rrl1476260r.2603a>g0.407
rrl1476262r.2605g>a0.571
rrl1476280r.2623a>c0.452
rrl1476281r.2624t>c0.533
rrl1476293r.2636c>t0.464
rrl1476294r.2637a>g0.464
rrl1476295r.2638c>g0.448
rrl1476296r.2639c>t0.414
rrl1476297r.2640c>a0.419
rrl1476311r.2654g>c0.500
rrl1476312r.2655t>c0.500
rrl1476313r.2656g>a0.488
rrl1476332r.2675g>c0.574
rrl1476338r.2681c>t0.607
rrl1476353r.2696g>a0.623
rrl1476358r.2701t>c0.590
rrl1476359r.2702c>t0.597
rrl1476382r.2725a>g0.735
rrl1476383r.2726t>a0.731
rrl1476408r.2751g>a0.778
rrl1476411r.2754g>a0.784
rrl1476425r.2768g>a0.744
rrl1476428r.2771c>t0.747
rrl1476463r.2806c>t0.750
rrl1476466r.2809c>t0.747
rrl1476470r.2813c>t0.753
rrl1476481r.2824t>c0.711
rrl1476506r.2849t>c0.658
rrl1476513r.2856g>a0.172
rrl1476529r.2872a>t0.833
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t0.923
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a0.929
rrl1476608r.2951c>g1.000
rrl1476616r.2959a>g0.929
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c0.900
rrl1476665r.3008t>a0.900
rrl1476674r.3017t>c0.900
rrl1476679r.3022t>a0.900

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;