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: 5cc55690f1986
Sample: 5cc55690f1986

Download results

Summary
ID: 5cc55690f1986
Date: Sun Apr 28 08:31:40 2019
Strain: lineage2;lineage1.2.1;lineage1.1.3
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.1.3Indo-OceanicEAI6RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6172c.933C>T1.000
gyrB6190c.951A>G1.000
gyrA7451c.150C>G1.000
gyrA7457c.156T>C1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>G1.000
gyrA7502c.201C>T1.000
gyrA7526c.225G>T1.000
gyrA7541c.240C>G1.000
gyrA7547c.246C>T1.000
gyrA7550c.249C>T1.000
gyrA7585p.Ser95Thr1.000
gyrA8324c.1023T>C1.000
gyrA8339c.1038A>G1.000
gyrA8340p.Ala347Ser1.000
gyrA8561c.1260A>C1.000
gyrA8585c.1284C>T1.000
gyrA8588c.1287G>A1.000
gyrA9338c.2037G>A1.000
rpoB760157c.351A>G1.000
rpoB760181c.375T>A1.000
rpoB760184c.378A>G1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760748c.942C>G1.000
rpoB761132c.1326G>T1.000
rpoB761133c.1327T>C1.000
rpoB761150c.1344A>C1.000
rpoB761168c.1362C>G1.000
rpoB761180c.1374A>C1.000
rpoB762962c.3156C>T1.000
rpoB762983c.3177C>G1.000
rpoB763031c.3225T>C1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763050c.3244C>T1.000
rpoB763055c.3249G>A1.000
rpoB763070c.3264T>C1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoC763570c.201G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763618c.249C>T1.000
rpoC763636c.267T>C1.000
rpoC763660c.291T>G1.000
rpoC763669c.300C>G1.000
rpoC763675c.306C>G1.000
rpoC763762c.393C>T1.000
rpoC763765c.396T>G1.000
rpoC763771c.402C>T1.000
rpoC763780c.411C>G1.000
rpoC764626c.1257C>T1.000
rpoC764746c.1377G>C1.000
rpoC764749c.1380G>C1.000
rpoC764752c.1383G>C1.000
rpoC764764c.1395T>C1.000
rpoC764782c.1413C>T1.000
rpoC764797c.1428G>C1.000
rpoC764803c.1434C>T1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764858c.1489T>C1.000
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764902c.1533C>T1.000
rpoC764911c.1542A>G1.000
rpoC764923c.1554A>G1.000
rpoC764932c.1563C>G1.000
rpoC764941c.1572G>A1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765622p.Glu751Asp1.000
rpoC766315c.2946C>G1.000
rpoC766321c.2952C>G1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766393c.3024C>G1.000
rpoC766402c.3033C>G1.000
rpoC766408c.3039C>T1.000
rpoC766426c.3057C>T1.000
rpoC766666c.3297C>G1.000
rpoC766672c.3303T>C1.000
rpoC766700c.3331C>T1.000
rpoC766726c.3357T>C1.000
rpoC766733c.3364C>T1.000
rpoC766738c.3369G>C1.000
rpoC766741c.3372G>C1.000
rpoC766750c.3381C>G1.000
rpoC766765c.3396A>C1.000
rpoC766774c.3405T>C1.000
rpoC766798c.3429C>G1.000
rpoC766801c.3432C>G1.000
rpoC766804c.3435A>G1.000
rpoC766843c.3474T>G1.000
rpoC766864c.3495G>C1.000
rpoC766876c.3507C>T1.000
rpoC766883p.Ser1172Ala1.000
rpoC766918c.3549C>T1.000
rpoC766933c.3564A>G1.000
rpoC766945c.3576A>G1.000
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpoC767263c.3894T>G1.000
rpoC767264p.Ala1299Gln1.000
rpoC767278c.3909T>C1.000
rpoC767281c.3912C>G1.000
rpoC767284c.3915C>T1.000
rpsL781658c.99A>G1.000
rpsL781682c.123T>C1.000
rpsL781715c.156T>C1.000
rpsL781718c.159C>G1.000
rpsL781721c.162C>T1.000
rpsL781728c.169T>C1.000
rpsL781736c.177T>C1.000
rpsL781751c.192G>C1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781766c.207C>T1.000
rpsL781772c.213C>G1.000
rpsL781793c.234G>C1.000
rpsL781859c.300T>G1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781883c.324G>A1.000
rpsL781886c.327C>T1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rpsL781933374G>A1.000
rrs1471970r.125g>a1.000
rrs1472030r.185g>t1.000
rrs1472031r.186g>t1.000
rrs1472033r.188a>g1.000
rrs1472034r.189t>c1.000
rrs1472040r.195t>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472489r.644a>g1.000
rrs1472686r.841g>a1.000
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473288r.1443c>t1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>t1.000
rrl1473806r.149c>t1.000
rrl1473813r.156c>t1.000
rrl1473831r.174g>a1.000
rrl1473876r.219g>a1.000
rrl1473887r.230t>a1.000
rrl1473888r.231t>a1.000
rrl1473899r.242a>t1.000
rrl1473918r.261c>t1.000
rrl1474130r.473c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474249r.592g>t1.000
rrl1474627r.970g>a1.000
rrl1474717r.1060a>t1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474783r.1126g>a1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474831r.1174a>g1.000
rrl1474945r.1288c>t1.000
rrl1474952r.1295acatcc>a1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>t1.000
rrl1475404r.1747a>g1.000
rrl1475405r.1748a>t1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>a1.000
rrl1475453r.1796t>a1.000
rrl1475480r.1823a>g1.000
rrl1475483r.1826c>t1.000
rrl1475487r.1830c>t1.000
rrl1475526r.1869c>a1.000
rrl1475599r.1942a>g1.000
rrl1475604r.1947a>c1.000
rrl1475605r.1948a>t1.000
rrl1475608r.1951t>c1.000
rrl1475617r.1960c>g1.000
rrl1475625r.1968g>c1.000
rrl1475637r.1980t>a1.000
rrl1475642r.1985t>c1.000
rrl1475657r.2000a>g1.000
rrl1475659r.2002g>a1.000
rrl1475760r.2103c>t1.000
rrl1476580r.2923g>a1.000
rrl1476597r.2940g>a1.000
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
rpsA1834231c.690T>G1.000
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834297c.756C>T1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834336c.795C>G1.000
rpsA1834348c.807T>C1.000
rpsA1834357c.816T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834375c.834G>A1.000
kasA2518735c.621C>T1.000
kasA2518747c.633C>G1.000
kasA2518768c.654C>G1.000
kasA2518783c.669T>C1.000
kasA2518789c.675G>C1.000
kasA2518795c.681C>A1.000
kasA2518798c.684G>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;