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: 5dc35bacdc45c
Sample: 5dc35bacdc45c

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Summary
ID: 5dc35bacdc45c
Date: Wed Nov 6 23:49:22 2019
Strain: lineage4.1.2.1;lineage2.2;lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB760115c.309C>T0.955
rpoB761213c.1407G>C0.139
rpoB761261c.1455G>C0.125
rpoB761264c.1458C>G0.128
rpoB762879p.Met1025Leu0.175
rpoB762899c.3093G>C0.179
rpoB762917c.3111C>G0.194
rpoB762923c.3117C>G0.216
rpoB762929c.3123G>C0.211
rpoB762959c.3153G>C0.211
rpoB762962c.3156C>T0.216
rpoB762989c.3183G>C0.186
rpoB762995c.3189G>T0.205
rpoB763005p.Cys1067Val0.118
rpoB763014p.Met1070Leu0.118
rpoB763017p.Gln1071Glu0.118
rpoB763031c.3225T>C0.156
rpoB763040c.3234C>G0.118
rpoB763052c.3246G>C0.143
rpoB763053c.3247T>C0.143
rpoB763067c.3261C>G0.146
rpoB763075p.Thr1090Ile0.140
rpoB763077p.Val1091Leu0.133
rpoC765150p.Gly594Glu0.889
rpoC765540p.Ala724Gly0.258
rpsL781395c.-165T>C1.000
rpsL781751c.192G>C0.159
rpsL781754c.195G>T0.156
rpsL781760c.201T>C0.156
rpsL781766c.207C>T0.156
rpsL781802c.243G>C0.163
rpsL781805c.246G>C0.163
rpsL781817c.258G>T0.140
rrs1472150r.305t>a0.125
rrs1472172r.327t>c0.139
rrs1472240r.395g>a0.194
rrs1472344r.499c>t0.293
rrs1472952r.1107t>c0.111
rrs1473035r.1190g>a0.132
rrl1474164r.507c>t0.174
rrl1474166r.509g>a0.174
rrl1474183r.526t>c0.174
rrl1474184r.527c>a0.174
rrl1474201r.544t>c0.179
rrl1474202r.545t>a0.184
rrl1474218r.561t>a0.302
rrl1474221r.564t>c0.133
rrl1474228r.571t>a0.149
rrl1474249r.592g>t0.237
rrl1474265r.608g>t0.222
rrl1474269r.612c>t0.211
rrl1474275r.618t>a0.211
rrl1474280r.623c>t0.216
rrl1474281r.624a>g0.216
rrl1474305r.648g>t0.320
rrl1474316r.659t>c0.296
rrl1474317r.660g>a0.296
rrl1474348r.691c>t0.250
rrl1474351r.694g>c0.267
rrl1474354r.697c>t0.267
rrl1474359r.702c>g0.250
rrl1474362r.705a>g0.250
rrl1474376r.719t>a0.161
rrl1474387r.730c>t0.226
rrl1474790r.1133c>t0.125
rrl1474794r.1137c>t0.125
rrl1474800r.1143t>c0.154
rrl1474823r.1166c>g0.139
rrl1474827r.1170c>t0.139
rrl1474831r.1174a>c0.139
rrl1474904r.1247g>c0.176
rrl1474905r.1248t>c0.176
rrl1474913r.1256t>c0.171
rrl1474920r.1263g>a0.167
rrl1475104r.1447t>a0.194
rrl1475114r.1457c>t0.200
rrl1475116r.1459g>a0.200
rrl1475124r.1467a>t0.212
rrl1475129r.1472g>a0.188
rrl1476359r.2702c>g0.158
rrl1476381r.2724g>c0.238
rrl1476428r.2771c>t0.200
rrl1476466r.2809c>t0.245
rrl1476506r.2849t>c0.200
rrl1476515r.2858c>t0.188
rrl1476524r.2867c>a0.174
rrl1476525r.2868a>g0.152
rrl1476530r.2873c>t0.146
rrl1476536r.2879g>a0.146
rrl1476537r.2880a>g0.146
rrl1476538r.2881a>g0.146
rrl1476540r.2883c>t0.143
rrl1476544r.2887t>a0.146
rpsA1834177c.636A>C0.150
rpsA1834609c.1068T>C0.154
rpsA1834612c.1071G>C0.140
rpsA1834619c.1078T>C0.135
tlyA1917972c.33A>G1.000
ald3086788c.-32T>C0.975
alr3841652c.-232A>T0.353
alr3841654c.-234A>C0.367
alr3841662c.-242A>G0.360
alr3841663c.-243G>A0.380
embC4242643c.2781C>T1.000
embC4242803p.Val981Leu0.980
gid4407927p.Glu92Asp0.180

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;