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: 5dc3c8f66550e
Sample: 5dc3c8f66550e

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Summary
ID: 5dc3c8f66550e
Date: Thu Nov 7 07:36:22 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrpsL p.Lys43Arg (1.00), rrs r.799c>t (0.11)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB762863c.3057T>C0.167
rpoB762872p.Met1022Ile0.162
rpoB762878p.Ile1024Met0.167
rpoB762879p.Met1025Leu0.167
rpoB762896c.3090G>C0.194
rpoB762925p.Thr1040Ile0.179
rpoB762938c.3132G>C0.158
rpoB762939p.Met1045Leu0.162
rpoB762942p.Ile1046Val0.162
rpoB762953c.3147G>A0.167
rpoB762965c.3159T>C0.162
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C1.000
rrs1472102r.257g>a0.118
rrs1472106r.261g>a0.143
rrs1472112r.267c>t0.143
rrs1472113r.268t>c0.143
rrs1472150r.305t>a0.205
rrs1472160r.315c>t0.139
rrs1472172r.327t>c0.588
rrs1472181r.336g>a0.136
rrs1472210r.365a>t0.492
rrs1472214r.369c>g0.429
rrs1472215r.370a>g0.159
rrs1472225r.380c>a0.515
rrs1472234r.389t>c0.154
rrs1472235r.390g>c0.333
rrs1472240r.395g>c0.492
rrs1472242r.397c>t0.483
rrs1472251r.406g>c0.375
rrs1472252r.407g>a0.367
rrs1472259r.414c>a0.396
rrs1472344r.499c>t0.310
rrs1472389r.544g>a0.210
rrs1472390r.545t>a0.210
rrs1472391r.546c>t0.210
rrs1472494r.649a>g0.171
rrs1472496r.651t>a0.167
rrs1472498r.653c>t0.167
rrs1472558r.713g>a0.128
rrs1472569r.724g>a0.140
rrs1472581r.736a>t0.170
rrs1472597r.752g>a0.167
rrs1472598r.753a>c0.130
rrs1472599r.754g>t0.132
rrs1472607r.762g>a0.164
rrs1472616r.771g>a0.213
rrs1472655r.810g>t0.105
rrs1472713r.868t>c0.288
rrs1472716r.871c>t0.340
rrs1472734r.889c>t0.194
rrs1472741r.896g>a0.203
rrs1472742r.897c>t0.493
rrs1472744r.899a>g0.297
rrs1472767r.922g>a0.174
rrs1472781r.936c>t0.506
rrs1472785r.940g>t0.177
rrs1472786r.941c>g0.177
rrs1472793r.948a>t0.500
rrs1472803r.958t>a0.286
rrs1472812r.967a>c0.186
rrs1472814r.969g>a0.145
rrs1472887r.1042g>c0.411
rrs1472895r.1050c>t0.110
rrs1473121r.1276t>c0.111
rrs1473145r.1300c>t0.114
rrs1473163r.1318c>t0.209
rrs1473164r.1319c>g0.195
rrs1473166r.1321g>a0.143
rrs1473177r.1332g>a0.367
rrs1473192r.1347a>g0.351
rrs1473199r.1354ca>c0.370
rrs1473202r.1357c>t0.148
rrs1473204r.1359c>t0.145
rrs1473205r.1360t>c0.364
rrs1473226r.1381c>t0.145
rrs1473252r.1407t>c0.158
rrs1473259r.1414c>t0.132
rrs1473270r.1425g>a0.122
rrs1473352r.1507c>t0.105
rrl1474151r.494c>t0.176
rrl1474155r.498g>a0.143
rrl1474164r.507c>t0.128
rrl1474171r.514c>t0.125
rrl1474181r.524c>t0.133
rrl1474184r.527c>t0.133
rrl1474185r.528g>a0.133
rrl1474197r.540c>t0.146
rrl1474199r.542g>a0.146
rrl1474202r.545t>c0.146
rrl1474218r.561t>a0.123
rrl1474228r.571t>c0.135
rrl1474249r.592g>t0.320
rrl1474252r.595t>a0.140
rrl1474269r.612c>t0.133
rrl1474584r.927c>t0.111
rrl1474864r.1207c>t0.139
rrl1474883r.1226t>c0.122
rrl1474904r.1247g>c0.128
rrl1475699r.2042c>t0.103
rrl1475783r.2126t>g0.293
rrl1475791r.2134a>g0.145
rrl1475803r.2146t>c0.491
rrl1475804r.2147g>c0.491
rrl1475816r.2159c>g0.492
rrl1475817r.2160a>g0.492
rrl1475881r.2224t>c0.293
rrl1475883r.2226a>c0.189
rrl1475892r.2235a>c0.163
rrl1475894r.2237c>g0.167
rrl1475898r.2241a>g0.143
rrl1475899r.2242g>a0.125
rrl1475900r.2243a>g0.154
rrl1475904r.2247g>a0.136
rrl1475916r.2259c>g0.128
rrl1475937r.2280a>t0.154
rrl1475943r.2286g>a0.158
rrl1475952r.2295a>g0.167
rrl1475963r.2306g>t0.121
rrl1475970r.2313c>t0.121
rrl1475975r.2318c>t0.114
rrl1475977r.2320a>g0.114
rrl1475978r.2321c>t0.114
rrl1476164r.2507a>g0.115
rrl1476194r.2537a>g0.217
rrl1476200r.2543a>t0.227
rrl1476201r.2544c>t0.227
rrl1476214r.2557g>t0.200
rrl1476215r.2558c>t0.200
rrl1476224r.2567a>g0.174
rrl1476245r.2588c>t0.160
rrl1476252r.2595t>g0.154
rrl1476253r.2596a>g0.154
rrl1476256r.2599a>g0.154
rrl1476260r.2603a>g0.160
rrl1476281r.2624t>c0.130
rrl1476336r.2679c>t0.211
rrl1476337r.2680c>t0.171
rrl1476338r.2681c>t0.250
rrl1476356r.2699c>a0.154
rrl1476357r.2700t>c0.133
rrl1476358r.2701t>c0.196
rrl1476359r.2702c>g0.386
rrl1476369r.2712c>t0.222
rrl1476381r.2724g>c0.298
rrl1476382r.2725a>g0.211
rrl1476383r.2726t>a0.220
rrl1476384r.2727g>t0.137
rrl1476408r.2751g>a0.386
rrl1476411r.2754g>t0.263
rrl1476425r.2768g>t0.290
rrl1476428r.2771c>t0.147
rrl1476429r.2772a>c0.328
rrl1476442r.2785t>a0.254
rrl1476443r.2786g>t0.380
rrl1476455r.2798c>a0.359
rrl1476456r.2799a>t0.215
rrl1476463r.2806c>a0.235
rrl1476466r.2809c>t0.453
rrl1476470r.2813c>t0.250
rrl1476481r.2824t>c0.281
rrl1476483r.2826g>a0.175
rrl1476501r.2844c>t0.245
rrl1476506r.2849t>c0.409
rrl1476515r.2858c>t0.207
rrl1476524r.2867c>t0.185
rrl1476525r.2868a>g0.185
rrl1476530r.2873c>t0.185
rrl1476536r.2879g>a0.167
rrl1476539r.2882a>g0.167
rrl1476540r.2883c>g0.167
rrl1476547r.2890c>t0.179
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
fbiA3640377c.-166G>A0.963
alr3841662c.-242A>G0.239
alr3841663c.-243G>A0.265
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;