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: 5d27846c0f12b
Sample: 5d27846c0f12b

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Summary
ID: 5d27846c0f12b
Date: Thu Jul 11 19:49:05 2019
Strain: lineage4.8;lineage4.1.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.45), rrs r.1484g>t (0.28)
CapreomycinRrrs r.1402c>a (0.45), rrs r.1484g>t (0.28)
KanamycinRrrs r.1402c>a (0.45), rrs r.1484g>t (0.28)

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.1.1.1Euro-American (X-type)X2RD183

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
rpoB762929c.3123G>C0.128
rpoC763534c.165T>C0.138
rpoC763537c.168C>G0.133
rpoC763546c.177A>G0.129
rpsL781395c.-165T>C1.000
rrs1472122r.277g>t0.211
rrs1472123r.278a>t0.211
rrs1472124r.279c>t0.211
rrs1472150r.305t>a0.311
rrs1472160r.315c>t0.287
rrs1472225r.380c>g0.435
rrs1472240r.395g>a0.366
rrs1472251r.406g>c0.333
rrs1472279r.434t>g0.254
rrs1472344r.499c>t0.250
rrs1472368r.523a>g0.339
rrs1472396r.551a>t0.446
rrs1472400r.555c>t0.426
rrs1472412r.567a>g0.304
rrs1472507r.662c>a0.459
rrs1472522r.677t>g0.458
rrs1472557r.712g>a0.593
rrs1472571r.726g>t0.571
rrs1472581r.736a>c0.370
rrs1472582r.737g>t0.360
rrs1472584r.739a>t0.355
rrs1472585r.740a>c0.355
rrs1472623r.778a>c0.416
rrs1472647r.802c>t0.367
rrs1472673r.828t>g0.303
rrs1472675r.830t>c0.286
rrs1472677r.832c>a0.273
rrs1472682r.837t>a0.269
rrs1472683r.838t>c0.269
rrs1472687r.842a>t0.279
rrs1472707r.862a>t0.393
rrs1472767r.922g>c0.317
rrs1472790r.945t>c0.333
rrs1472812r.967a>t0.257
rrs1472973r.1128a>t0.342
rrs1472996r.1151t>c0.378
rrs1473066r.1221a>g0.486
rrs1473081r.1236c>t0.425
rrs1473145r.1300c>t0.235
rrs1473164r.1319c>t0.285
rrs1473166r.1321g>a0.299
rrs1473226r.1381c>g0.478
rrs1473259r.1414c>t0.421
rrs1473276r.1431a>g0.322
rrs1473288r.1443c>g0.153
rrs1473290r.1445c>t0.150
rrs1473292r.1447g>t0.150
rrs1473294r.1449a>g0.153
rrs1473301r.1456t>c0.255
rrs1473315r.1470t>c0.196
rrs1473316r.1471c>t0.200
rrs1473319r.1474c>t0.196
rrs1473324r.1479g>a0.232
rrl1473862r.205c>t0.341
rrl1473876r.219g>a0.341
rrl1473887r.230t>g0.385
rrl1473898r.241c>t0.324
rrl1473899r.242a>g0.324
rrl1473916r.259c>a0.486
rrl1473922r.265a>g0.471
rrl1473923r.266c>g0.471
rrl1474001r.344c>t1.000
rrl1474166r.509g>t0.182
rrl1474167r.510t>c0.136
rrl1474184r.527c>t0.125
rrl1474186r.529a>g0.129
rrl1474197r.540c>t0.250
rrl1474202r.545t>g0.245
rrl1474218r.561t>g0.278
rrl1474253r.596a>t0.241
rrl1474264r.607t>g0.135
rrl1474265r.608g>t0.135
rrl1474266r.609t>c0.135
rrl1474269r.612c>a0.135
rrl1474271r.614a>g0.128
rrl1474467r.810a>t0.286
rrl1474476r.819c>t0.233
rrl1474488r.831g>a0.224
rrl1474496r.839c>t0.246
rrl1474497r.840g>c0.246
rrl1474506r.849c>g0.239
rrl1474507r.850g>t0.242
rrl1474516r.859c>t0.292
rrl1474529r.872a>c0.286
rrl1474530r.873g>a0.286
rrl1474537r.880g>a0.229
rrl1474539r.882c>t0.225
rrl1474540r.883t>g0.232
rrl1474552r.895c>t0.443
rrl1474558r.901g>a0.455
rrl1474582r.925t>a0.462
rrl1474760r.1103a>g0.170
rrl1474794r.1137c>t0.185
rrl1474798r.1141c>t0.182
rrl1474806r.1149a>c0.185
rrl1474823r.1166c>g0.262
rrl1474827r.1170c>t0.250
rrl1474830r.1173a>g0.254
rrl1474831r.1174a>t0.258
rrl1474853r.1196a>g0.434
rrl1474864r.1207c>t0.418
rrl1474904r.1247g>c0.224
rrl1474905r.1248t>c0.221
rrl1475699r.2042c>t0.217
rrl1475722r.2065g>t0.279
rrl1475869r.2212c>a0.408
rrl1475877r.2220c>t0.253
rrl1475881r.2224t>c0.250
rrl1475883r.2226a>t0.250
rrl1475892r.2235a>c0.333
rrl1475898r.2241a>g0.257
rrl1475899r.2242g>a0.257
rrl1475906r.2249c>t0.303
rrl1475916r.2259c>t0.338
rrl1475943r.2286g>a0.417
rrl1475952r.2295a>g0.475
rrl1475970r.2313c>t0.214
rrl1475975r.2318c>t0.214
rrl1475977r.2320a>g0.200
rrl1475978r.2321c>t0.200
rrl1475988r.2331a>g0.238
rrl1475991r.2334t>a0.238
rrl1475993r.2336c>t0.238
rrl1475996r.2339t>g0.227
rrl1476130r.2473g>a0.225
rrl1476131r.2474c>t0.250
rrl1476141r.2484a>g0.254
rrl1476153r.2496t>c0.228
rrl1476164r.2507a>g0.227
rrl1476165r.2508t>g0.227
rrl1476194r.2537a>g0.344
rrl1476200r.2543a>t0.304
rrl1476201r.2544c>t0.298
rrl1476204r.2547c>t0.293
rrl1476215r.2558c>t0.439
rrl1476224r.2567a>g0.483
rrl1476235r.2578a>g0.243
rrl1476245r.2588c>t0.182
rrl1476359r.2702c>g0.306
rrl1476363r.2706a>g0.294
rrl1476366r.2709a>c0.294
rrl1476368r.2711t>c0.278
rrl1476369r.2712c>t0.278
rrl1476374r.2717t>g0.270
rrl1476381r.2724g>c0.412
rrl1476428r.2771c>t0.383
rrl1476429r.2772a>c0.390
rrl1476481r.2824t>c0.312
rrl1476506r.2849t>c0.286
rrl1476515r.2858c>t0.245
rrl1476572r.2915g>t0.128
rrl1476573r.2916a>g0.128
rpsA1833558p.Val6Asp0.158
tlyA1917972c.33A>G1.000
folC2746832p.Val256Gly0.400
thyX3068015c.-70T>G0.190
alr3841662c.-242A>G0.500
alr3841663c.-243G>A0.219
embC4242643c.2781C>T1.000
embB4246544p.Thr11Pro0.200
embB4246548p.Pro12Gln0.357
embB4246555c.42G>C0.500
embB4246556p.Ala15Pro0.500
embB4246563p.Leu17Trp0.500
embB4246567c.54G>T0.316

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;