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: 5cc522d2d1a72
Sample: 5cc522d2d1a72

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Summary
ID: 5cc522d2d1a72
Date: Sun Apr 28 04:51:09 2019
Strain: lineage2;lineage1.1;lineage4.3.2.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage4.3.2.1Euro-American (LAM)LAM3RD761

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rpoB760199c.393C>G1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760244c.438G>C1.000
rpoB760253c.447T>C1.000
rpoB760256c.450C>T1.000
rpoB760274p.Glu156Asp1.000
rpoB760283c.477G>C1.000
rpoB762221c.2415G>A1.000
rpoB762233c.2427G>C1.000
rpoB762236c.2430G>C1.000
rpoB762254c.2448T>C0.923
rpoB762257c.2451C>G1.000
rpoB762290c.2484C>T1.000
rpoB762962c.3156C>T1.000
rpoB762989c.3183G>T1.000
rpoB762995c.3189G>C1.000
rpoB762998c.3192G>A1.000
rpoB763004c.3198G>A1.000
rpoC763453c.84C>G1.000
rpoC763456c.87A>G1.000
rpoC763459c.90G>A1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763505c.136C>T1.000
rpoC763528c.159G>T1.000
rpoC763531c.162G>C1.000
rpoC763534c.165T>C1.000
rpoC763537c.168C>G1.000
rpoC763546c.177A>G1.000
rpoC763558c.189C>T1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763594c.225C>T1.000
rpoC763597c.228G>A1.000
rpoC763621c.252C>T1.000
rpoC763624c.255C>G1.000
rpoC763633c.264T>C1.000
rpoC763651c.282C>T1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>C1.000
rpoC763669c.300C>G1.000
rpoC764858c.1489T>C1.000
rpoC764869c.1500C>T1.000
rpoC764872c.1503A>G1.000
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764893c.1524T>C1.000
rpoC764896c.1527C>T1.000
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln1.000
rpoC764920c.1551G>C1.000
rpoC764926c.1557C>T1.000
rpoC764935c.1566T>C1.000
rpoC764948c.1579T>C1.000
rpoC764953c.1584G>C1.000
rpoC764968c.1599T>C1.000
rpoC765007c.1638T>G1.000
rpoC765008c.1639T>C1.000
rpoC765011c.1642A>T1.000
rpoC765016c.1647C>G1.000
rpoC765019c.1650A>G1.000
rpoC765034c.1665T>C1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765055c.1686C>G1.000
rpoC765076c.1707A>G1.000
rpoC765079c.1710T>C1.000
rpoC765082c.1713G>C1.000
rpoC765085c.1716T>C1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>T1.000
rpoC765811c.2442T>C1.000
rpoC765814c.2445A>T1.000
rpoC765817c.2448G>C1.000
rpoC765820c.2451G>C1.000
rpoC765823c.2454C>G1.000
rpoC765844c.2475C>G1.000
rpoC765871c.2502T>G1.000
rpoC765875p.Val836Ile1.000
rpoC765886c.2517C>G1.000
rpoC765907c.2538G>T1.000
rpoC765910c.2541G>C1.000
rpoC765934c.2565C>T1.000
rpoC765940c.2571A>T1.000
rpoC766996c.3627C>T1.000
rpoC767002c.3633G>C1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781769c.210G>A1.000
rpsL781802c.243G>C1.000
rpsL781805c.246G>C1.000
rpsL781814c.255C>T1.000
rpsL781817c.258G>T1.000
rpsL781829c.270G>T1.000
rpsL781832c.273T>C1.000
rpsL781853c.294C>T1.000
rrs1471914r.69a>g1.000
rrs1471918r.73a>t1.000
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471934r.89a>g1.000
rrs1471938r.93t>a1.000
rrs1471943r.98t>c1.000
rrs1471978r.133c>t1.000
rrs1471985r.140t>c1.000
rrs1471986r.141c>t1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472148r.303t>c1.000
rrs1472150r.305t>a1.000
rrs1472172r.327t>c1.000
rrs1472225r.380c>g1.000
rrs1472251r.406g>a1.000
rrs1472416r.571c>t1.000
rrs1472422r.577t>c1.000
rrs1472425r.580t>c1.000
rrs1472435r.590t>c1.000
rrs1472437r.592t>a1.000
rrs1472446r.601t>a1.000
rrs1472450r.605a>g1.000
rrs1472451r.606c>g1.000
rrs1472456r.611t>c1.000
rrs1472460r.615t>c1.000
rrs1472461r.616g>c1.000
rrs1472462r.617t>c1.000
rrs1472467r.622g>t1.000
rrs1472473r.628g>t1.000
rrs1472486r.641a>g1.000
rrs1472489r.644a>t1.000
rrs1472497r.652g>t1.000
rrs1472530r.685g>a1.000
rrs1472580r.735c>a1.000
rrs1472597r.752g>a1.000
rrs1472612r.767g>t1.000
rrs1472682r.837t>a1.000
rrs1472683r.838t>c1.000
rrs1472873r.1028c>t1.000
rrs1472875r.1030t>g1.000
rrs1472880r.1035g>a1.000
rrs1472953r.1108g>a1.000
rrs1472957r.1112c>t1.000
rrs1472969r.1124a>g1.000
rrs1472978r.1133t>c1.000
rrs1473026r.1181t>c1.000
rrs1473088r.1243a>g1.000
rrs1473100r.1255g>a1.000
rrs1473104r.1259c>t1.000
rrs1473110r.1265t>g1.000
rrs1473111r.1266a>g1.000
rrs1473121r.1276t>c0.932
rrs1473123r.1278a>t1.000
rrs1473173r.1328c>t1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>gt1.000
rrs1473301r.1456t>c1.000
rrl1473696r.39t>c1.000
rrl1473698r.41g>a1.000
rrl1473699r.42a>g1.000
rrl1473717r.60g>a1.000
rrl1473731r.74t>a1.000
rrl1473756r.99g>t1.000
rrl1473757r.100t>g1.000
rrl1473758r.101g>t1.000
rrl1473768r.111a>g1.000
rrl1473770r.113t>g1.000
rrl1473806r.149c>t1.000
rrl1473814r.157a>c1.000
rrl1473815r.158t>a0.923
rrl1473816r.159c>g1.000
rrl1473833r.176g>t1.000
rrl1473844r.187c>t1.000
rrl1474135r.478g>a1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g1.000
rrl1474183r.526t>c1.000
rrl1474184r.527c>t1.000
rrl1474186r.529a>g1.000
rrl1474201r.544t>c1.000
rrl1474218r.561t>a1.000
rrl1474249r.592g>t1.000
rrl1474266r.609t>c1.000
rrl1474269r.612c>t1.000
rrl1474283r.626a>g1.000
rrl1474348r.691c>t1.000
rrl1474351r.694g>t1.000
rrl1474353r.696a>g1.000
rrl1474359r.702c>g1.000
rrl1474362r.705a>g1.000
rrl1474387r.730c>t1.000
rrl1474402r.745t>c1.000
rrl1474454r.797g>a1.000
rrl1474496r.839c>a1.000
rrl1474497r.840g>c1.000
rrl1474506r.849c>g1.000
rrl1474507r.850g>t0.950
rrl1474537r.880g>a1.000
rrl1474717r.1060a>g1.000
rrl1474722r.1065t>c1.000
rrl1474734r.1077g>t1.000
rrl1474749r.1092c>t1.000
rrl1474753r.1096ac>a1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t0.976
rrl1474803r.1146g>a1.000
rrl1474812r.1155g>a1.000
rrl1474823r.1166c>g1.000
rrl1474824r.1167a>g1.000
rrl1474825r.1168g>a1.000
rrl1474827r.1170c>t1.000
rrl1474830r.1173a>g1.000
rrl1474831r.1174a>c1.000
rrl1474837r.1180a>g1.000
rrl1474896r.1239a>g1.000
rrl1474903r.1246t>c1.000
rrl1474904r.1247g>c1.000
rrl1474913r.1256t>c1.000
rrl1474932r.1275c>t1.000
rrl1475065r.1408g>a1.000
rrl1475067r.1410a>g1.000
rrl1475076r.1419c>a1.000
rrl1475079r.1422t>c1.000
rrl1475081r.1424c>t1.000
rrl1475090r.1433a>t1.000
rrl1475113r.1456c>t1.000
rrl1475114r.1457c>t1.000
rrl1475116r.1459g>a1.000
rrl1475419r.1762c>t1.000
rrl1475422r.1765a>g1.000
rrl1475429r.1772g>a1.000
rrl1475443r.1786g>a1.000
rrl1475452r.1795c>a1.000
rrl1475460r.1803a>g1.000
rrl1475475r.1818c>t1.000
rrl1475479r.1822c>t1.000
rrl1475480r.1823a>t1.000
rrl1475481r.1824c>g1.000
rrl1475482r.1825a>g1.000
rrl1475483r.1826c>t1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475538r.1881t>a1.000
rrl1475539r.1882a>t1.000
rrl1475545r.1888t>g1.000
rrl1475550r.1893a>g1.000
rrl1475555r.1898t>c1.000
rrl1475659r.2002g>a1.000
rrl1475699r.2042c>t1.000
rrl1475791r.2134a>g1.000
rrl1475883r.2226a>t1.000
rrl1475884r.2227a>g1.000
rrl1475892r.2235a>g1.000
rrl1475897r.2240t>c1.000
rrl1475916r.2259c>t1.000
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475988r.2331a>g1.000
rrl1476030r.2373a>g1.000
rrl1476032r.2375c>a1.000
rrl1476034r.2377c>g1.000
rrl1476035r.2378g>c1.000
rrl1476044r.2387t>g1.000
rrl1476045r.2388g>t1.000
rrl1476047r.2390g>t1.000
rrl1476049r.2392c>t1.000
rrl1476058r.2401t>c1.000
rrl1476076r.2419a>g1.000
rrl1476086r.2429g>a1.000
rrl1476088r.2431a>c1.000
rrl1476099r.2442a>g1.000
rrl1476103r.2446c>a1.000
rrl1476105r.2448ga>g1.000
rrl1476110r.2453g>t1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476160r.2503t>c1.000
rrl1476194r.2537a>g1.000
rrl1476200r.2543a>t1.000
rrl1476201r.2544c>t1.000
rrl1476214r.2557g>t1.000
rrl1476221r.2564t>c1.000
rrl1476224r.2567a>g1.000
rrl1476245r.2588c>t1.000
rrl1476251r.2594t>a1.000
rrl1476252r.2595t>g1.000
rrl1476256r.2599a>t1.000
rrl1476260r.2603a>g1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>g1.000
rrl1476298r.2641c>g1.000
rrl1476300r.2643g>a1.000
rrl1476301r.2644a>t1.000
rrl1476309r.2652g>c1.000
rrl1476428r.2771c>t1.000
rrl1476524r.2867c>t1.000
rrl1476525r.2868a>g1.000
rrl1476539r.2882a>g1.000
rrl1476540r.2883c>g1.000
rrl1476584r.2927c>t1.000
rrl1476585r.2928a>g1.000
rrl1476608r.2951c>g1.000
rrl1476614r.2957a>t1.000
rrl1476616r.2959a>g1.000
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
rrl1476629r.2972c>a1.000
rrl1476630r.2973a>g1.000
rrl1476661r.3004a>g1.000
rrl1476665r.3008t>g1.000
rrl1476666r.3009c>t1.000
rpsA1833964c.423C>T1.000
rpsA1833970c.429G>T1.000
rpsA1833979c.438T>C1.000
rpsA1833991c.450C>G1.000
rpsA1834012c.471G>C1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834051c.510G>A1.000
rpsA1834093c.552G>T1.000
rpsA1834099c.558C>G1.000
rpsA1834102c.561T>C1.000
rpsA1834105c.564C>T1.000
rpsA1834144c.603G>A1.000
rpsA1834186c.645C>G1.000
rpsA1834189c.648G>C1.000
rpsA1834213c.672G>C1.000
rpsA1834234c.693G>C1.000
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834279c.738C>T1.000
rpsA1834298p.Gln253Glu1.000
rpsA1834340p.Met267Leu1.000
rpsA1834399p.His286Gln1.000
rpsA1834411c.870T>C1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C1.000
rpsA1834465c.924T>C1.000
rpsA1834468c.927A>G1.000

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.

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