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.
Back to results page.
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: 5dca10d518580
Sample: 5dca10d518580

Download results

Summary
ID: 5dca10d518580
Date: Tue Nov 12 01:57:01 2019
Strain: lineage2.2.1
Drug-resistance: XDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRfabG1 c.-15C>T (1.00), inhA p.Ile21Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00), rpoB p.Ile480Val (1.00)
EthambutolRembB p.Met306Ile (1.00)
PyrazinamideRpncA c.534 535insG (0.93)
StreptomycinRrpsL p.Lys43Arg (1.00), rrs r.888g>a (0.30)
EthionamideRfabG1 c.-15C>T (1.00), inhA p.Ile21Thr (1.00)
FluoroquinolonesRgyrA p.Ala90Val (0.98)
AmikacinRrrs r.1401a>g (0.72)
CapreomycinRrrs r.1401a>g (0.72)
KanamycinRrrs r.1401a>g (0.72)

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
gyrA8352p.Gly351Arg1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpoC767145p.Pro1259Leu0.872
rpsL781395c.-165T>C1.000
rplC801270c.462T>C1.000
rrs1472108r.263c>t0.119
rrs1472123r.278a>g0.136
rrs1472124r.279c>t0.159
rrs1472137r.292g>a0.207
rrs1472150r.305t>a0.269
rrs1472151r.306c>t0.235
rrs1472172r.327t>c0.356
rrs1472203r.358g>a0.196
rrs1472225r.380c>a0.125
rrs1472251r.406g>a0.179
rrs1472258r.413a>g0.140
rrs1472259r.414c>a0.209
rrs1472513r.668t>c0.132
rrs1472530r.685g>a0.167
rrs1472537r.692c>t0.152
rrs1472544r.699c>a0.140
rrs1472545r.700a>t0.136
rrs1472549r.704g>a0.133
rrs1472566r.721g>a0.146
rrs1472571r.726g>c0.204
rrs1472579r.734g>t0.146
rrs1472581r.736a>t0.255
rrs1472584r.739a>t0.107
rrs1472598r.753a>c0.304
rrs1472599r.754g>t0.246
rrs1472616r.771g>a0.293
rrs1472697r.852t>c0.172
rrs1472713r.868t>c0.222
rrs1472716r.871c>t0.222
rrs1472742r.897c>t0.313
rrs1472744r.899a>g0.324
rrs1472781r.936c>t0.391
rrs1472793r.948a>t0.350
rrs1472803r.958t>a0.311
rrs1472895r.1050c>t0.318
rrs1473035r.1190g>a0.135
rrs1473177r.1332g>a0.171
rrs1473202r.1357c>t0.101
rrs1473352r.1507c>t0.240
rrl1474218r.561t>a0.125
rrl1474228r.571t>c0.100
rrl1474249r.592g>t0.150
rrl1474252r.595t>a0.105
rrl1474488r.831g>t0.128
rrl1474508r.851c>t0.114
rrl1474516r.859c>a0.156
rrl1474527r.870t>c0.163
rrl1474537r.880g>a0.167
rrl1474542r.885a>g0.163
rrl1474658r.1001a>g0.135
rrl1474663r.1006c>t0.167
rrl1474673r.1016t>c0.167
rrl1474676r.1019t>a0.159
rrl1474677r.1020a>g0.159
rrl1474692r.1035g>a0.229
rrl1474712r.1055g>t0.196
rrl1474734r.1077g>t0.177
rrl1474754r.1097c>g0.179
rrl1474760r.1103a>g0.172
rrl1474794r.1137c>t0.163
rrl1475171r.1514c>t0.122
rrl1475172r.1515a>g0.122
rrl1475783r.2126t>g0.228
rrl1475803r.2146t>c0.276
rrl1475804r.2147g>c0.281
rrl1475816r.2159c>g0.296
rrl1475817r.2160a>g0.302
rrl1475858r.2201t>c0.273
rrl1475866r.2209t>a0.255
rrl1476332r.2675g>c0.250
rrl1476338r.2681c>t0.250
rrl1476353r.2696g>t0.265
rrl1476358r.2701t>c0.273
rrl1476369r.2712c>t0.340
rrl1476372r.2715t>c0.327
rrl1476382r.2725a>g0.339
rrl1476383r.2726t>a0.365
rrl1476425r.2768g>t0.355
rrl1476428r.2771c>t0.377
rrl1476429r.2772a>c0.365
rrl1476466r.2809c>t0.128
rrl1476481r.2824t>c0.347
rrl1476506r.2849t>c0.328
rrl1476536r.2879g>a0.132
rrl1476538r.2881a>g0.128
rrl1476584r.2927c>t0.154
rrl1476585r.2928a>g0.128
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
alr3840952p.Lys157Glu0.714
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;