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: 5cc54cfe9a222
Sample: 5cc54cfe9a222

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Summary
ID: 5cc54cfe9a222
Date: Sun Apr 28 07:50:27 2019
Strain: lineage2;lineage4.3.2.1;lineage3.1.2.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage3.1.2.2East-African-IndianCASRD750

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rpoB760916c.1110C>T1.000
rpoB760919c.1113C>T1.000
rpoB760928c.1122G>C1.000
rpoB760946c.1140A>G1.000
rpoB760958c.1152G>C1.000
rpoB761282c.1476C>T1.000
rpoB762086c.2280G>C1.000
rpoB762098c.2292C>G1.000
rpoB762929c.3123G>T1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>C1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763615c.246G>C1.000
rpoC763619p.Arg84Lys1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>C1.000
rpoC763669c.300C>G1.000
rpoC763675c.306C>G1.000
rpoC764278c.909A>G1.000
rpoC764284c.915G>C1.000
rpoC764297p.Met310Leu1.000
rpoC764320c.951C>G1.000
rpoC764341c.972G>C1.000
rpoC764344c.975C>T1.000
rpoC764560c.1191T>C1.000
rpoC764575c.1206T>G1.000
rpoC764578c.1209C>G1.000
rpoC764602c.1233C>T1.000
rpoC764605c.1236G>T1.000
rpoC764611c.1242G>T1.000
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T1.000
rpoC764662c.1293G>C1.000
rpoC764668c.1299C>T1.000
rpoC764686c.1317C>T1.000
rpoC764701c.1332C>G1.000
rpoC764713c.1344G>A1.000
rpoC764716c.1347G>C1.000
rpoC764746c.1377G>T1.000
rpoC764749c.1380G>C1.000
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G1.000
rpoC764764p.His465Gln1.000
rpoC764767c.1398G>A1.000
rrs1471934r.89a>g1.000
rrs1471979r.134t>c0.833
rrs1471980r.135g>t0.833
rrs1471981r.136c>g1.000
rrs1471985r.140t>c0.250
rrs1471986r.141c>t1.000
rrs1472075r.230a>g1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472137r.292g>a1.000
rrs1472150r.305t>a1.000
rrs1472151r.306c>t1.000
rrs1472172r.327t>c1.000
rrs1472251r.406g>a1.000
rrs1472382r.537g>a1.000
rrs1472422r.577t>c1.000
rrs1472471r.626g>a1.000
rrs1472489r.644a>t1.000
rrs1472497r.652g>a1.000
rrs1472530r.685g>a1.000
rrs1472580r.735c>t1.000
rrs1472612r.767g>t1.000
rrs1472675r.830t>c0.481
rrs1472677r.832c>t0.500
rrs1472680r.835c>t1.000
rrs1472682r.837t>a1.000
rrs1472683r.838t>c1.000
rrs1472686r.841g>a1.000
rrs1472836r.991g>a1.000
rrs1472873r.1028c>t1.000
rrs1472874r.1029c>t1.000
rrs1472875r.1030t>g1.000
rrs1472880r.1035g>a1.000
rrs1472956r.1111t>c1.000
rrs1472990r.1145a>g1.000
rrs1473081r.1236c>t1.000
rrs1473088r.1243a>g1.000
rrs1473099r.1254t>g1.000
rrs1473100r.1255g>a1.000
rrs1473104r.1259c>t1.000
rrs1473110r.1265t>g1.000
rrs1473111r.1266a>g1.000
rrs1473121r.1276t>c1.000
rrs1473123r.1278a>t0.958
rrs1473130r.1285g>a1.000
rrs1473145r.1300c>t1.000
rrs1473166r.1321g>a1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>gt1.000
rrl1473743r.86c>t1.000
rrl1473750r.93c>a1.000
rrl1473756r.99g>t1.000
rrl1473757r.100t>g1.000
rrl1473758r.101g>t1.000
rrl1473768r.111a>g1.000
rrl1473770r.113t>g1.000
rrl1473844r.187c>t1.000
rrl1473870r.213g>a1.000
rrl1473876r.219g>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1473922r.265a>g1.000
rrl1473923r.266c>g1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g1.000
rrl1474181r.524c>t1.000
rrl1474183r.526t>c1.000
rrl1474184r.527c>t1.000
rrl1474186r.529a>g1.000
rrl1474201r.544t>c1.000
rrl1474218r.561t>a1.000
rrl1474249r.592g>t1.000
rrl1474348r.691c>t1.000
rrl1474351r.694g>t0.900
rrl1474353r.696a>c0.900
rrl1474359r.702c>g1.000
rrl1474362r.705a>g1.000
rrl1474387r.730c>t1.000
rrl1474496r.839c>t1.000
rrl1474497r.840g>c1.000
rrl1474506r.849c>g1.000
rrl1474507r.850g>t0.952
rrl1474529r.872a>c1.000
rrl1474530r.873g>a1.000
rrl1474537r.880g>a1.000
rrl1474539r.882c>t1.000
rrl1474540r.883t>g1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a1.000
rrl1474812r.1155g>a1.000
rrl1474823r.1166c>g1.000
rrl1474824r.1167a>g1.000
rrl1474830r.1173a>g1.000
rrl1474903r.1246t>c1.000
rrl1474904r.1247g>c1.000
rrl1474913r.1256t>c1.000
rrl1475090r.1433a>t1.000
rrl1475114r.1457c>t1.000
rrl1475116r.1459g>a1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475538r.1881t>a1.000
rrl1475539r.1882a>t1.000
rrl1475545r.1888t>g1.000
rrl1475550r.1893a>g1.000
rrl1475649r.1992a>g1.000
rrl1475655r.1998t>a1.000
rrl1475659r.2002g>a1.000
rrl1475699r.2042c>t1.000
rrl1475769r.2112t>c1.000
rrl1475775r.2118g>t1.000
rrl1475883r.2226a>t1.000
rrl1475884r.2227a>g1.000
rrl1475897r.2240t>c1.000
rrl1475916r.2259c>g1.000
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475988r.2331a>g1.000
rrl1475997r.2340a>t1.000
rrl1476086r.2429g>a1.000
rrl1476088r.2431a>t1.000
rrl1476099r.2442a>g1.000
rrl1476105r.2448ga>g1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476194r.2537a>g1.000
rrl1476200r.2543a>t1.000
rrl1476201r.2544c>t1.000
rrl1476214r.2557g>t0.967
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g1.000
rrl1476245r.2588c>t1.000
rrl1476251r.2594t>g1.000
rrl1476256r.2599a>t1.000
rrl1476260r.2603a>g1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>a1.000
rrl1476298r.2641c>a1.000
rrl1476301r.2644a>t1.000
rrl1476309r.2652g>t1.000
rrl1476428r.2771c>t1.000
rrl1476524r.2867c>t1.000
rrl1476584r.2927c>t1.000
rrl1476585r.2928a>g1.000
rrl1476594r.2937c>t1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>t1.000
rrl1476614r.2957a>t1.000
rpsA1833874c.333T>C1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833904c.363G>A1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833961c.420C>G1.000
rpsA1833979c.438T>C1.000
rpsA1834451c.910T>C1.000
rpsA1834468c.927A>G1.000
rpsA1834483p.Glu314Asp1.000
rpsA1834486p.Glu315Asp1.000
rpsA1834489c.948T>C1.000
rpsA1834498c.957C>T1.000
rpsA1834501c.960G>C1.000
rpsA1834528c.987T>C1.000
rpsA1834600c.1059G>C1.000
rpsA1834606c.1065C>T1.000
rpsA1834612c.1071G>C1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000

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;