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: 5cc55f2668517
Sample: 5cc55f2668517

Download results

Summary
ID: 5cc55f2668517
Date: Sun Apr 28 09:08:31 2019
Strain: root
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (0.91)
Pyrazinamide
StreptomycinRrrs r.190g>a (1.00), rrs r.462c>t (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7391c.90C>T0.900
gyrA7412c.111C>G0.900
gyrA7430c.129G>A0.900
gyrA7433c.132G>C0.900
gyrA7442c.141G>C0.900
gyrA7457c.156T>C0.900
gyrA7547c.246C>T0.900
gyrA7550c.249C>T0.917
gyrA7585p.Ser95Thr1.000
gyrA9296c.1995T>C1.000
gyrA9304p.Gly668Asp1.000
gyrA9308p.Asp669Glu1.000
rpoB759570c.-237C>CG0.900
rpoB760235c.429T>C1.000
rpoB760298c.492G>C0.938
rpoB760310c.504G>C0.929
rpoB760313c.507G>C0.923
rpoB760328c.522G>C0.917
rpoB760331c.525G>C0.917
rpoB760337c.531C>G0.909
rpoB760340c.534G>T0.846
rpoB760361c.555T>C0.846
rpoB760376p.Asp190Glu0.846
rpoB760381p.Thr192Met0.833
rpoB760919c.1113C>G0.929
rpoB760925c.1119T>C0.933
rpoB760928c.1122G>C0.938
rpoB760946c.1140A>G1.000
rpoB760970c.1164G>C1.000
rpoB760973c.1167G>C1.000
rpoB760991c.1185G>C1.000
rpoB761006c.1200C>T1.000
rpoB761015c.1209G>C1.000
rpoB761057c.1251G>C1.000
rpoB761213c.1407G>C1.000
rpoB761234c.1428G>C1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G0.917
rpoB761258c.1452G>A0.917
rpoB761261c.1455G>T0.917
rpoB761264c.1458C>G0.917
rpoB761273c.1467T>C0.923
rpoB761318c.1512G>C0.900
rpoB761327c.1521A>G0.900
rpoB761510c.1704T>C1.000
rpoB761537c.1731C>T0.933
rpoB761570c.1764T>C0.917
rpoB761573c.1767C>G0.917
rpoB761579c.1773G>C0.909
rpoB761606c.1800C>G0.900
rpoB761834c.2028T>C1.000
rpoB762011c.2205G>C1.000
rpoB762029c.2223C>G1.000
rpoB762053c.2247T>C1.000
rpoB762056c.2250G>A1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762114p.Ile770Val1.000
rpoB762131c.2325C>G1.000
rpoB762134c.2328C>G1.000
rpoB762143c.2337T>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762209c.2403C>T1.000
rpoB762212c.2406G>C1.000
rpoB762233c.2427G>C1.000
rpoB762254c.2448T>C1.000
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762296c.2490G>A1.000
rpoB762449c.2643C>A1.000
rpoB762470c.2664G>C1.000
rpoB762491c.2685T>G1.000
rpoB762507p.Leu901Met0.900
rpoB762510p.Ala902Pro0.900
rpoB762813p.Met1003Val1.000
rpoB762818c.3012C>G1.000
rpoB762827c.3021G>T1.000
rpoB762839c.3033G>A1.000
rpoB762857c.3051C>G1.000
rpoB762920c.3114C>T1.000
rpoB762926c.3120C>G1.000
rpoB762929c.3123G>T1.000
rpoB762995c.3189G>T1.000
rpoB763013c.3207C>G1.000
rpoB763034c.3228C>A1.000
rpoC763456c.87A>G0.900
rpoC763468c.99G>C0.909
rpoC763486c.117T>C0.917
rpoC763492c.123G>C0.923
rpoC763546c.177A>G0.889
rpoC763570c.201G>C0.875
rpoC763594c.225C>T0.917
rpoC763603c.234C>T0.917
rpoC763618c.249C>T0.917
rpoC763624c.255C>G0.923
rpoC763633c.264T>C0.917
rpoC763660c.291T>G0.900
rpoC763666c.297G>C0.900
rpoC763669c.300C>G0.900
rpoC764152c.783C>T1.000
rpoC764159c.790C>T1.000
rpoC764485c.1116G>C1.000
rpoC764497c.1128A>G1.000
rpoC764605c.1236G>C0.818
rpoC764611c.1242G>T0.857
rpoC764632c.1263T>C0.824
rpoC764650c.1281G>T0.850
rpoC764713c.1344G>A0.900
rpoC764716c.1347G>C0.900
rpoC764746c.1377G>C0.920
rpoC764764c.1395T>C1.000
rpoC764803c.1434C>T1.000
rpoC764932c.1563C>G1.000
rpoC765421c.2052C>G1.000
rpoC765451c.2082C>T1.000
rpoC765454c.2085C>G1.000
rpoC765478c.2109T>C1.000
rpoC765496c.2127C>T1.000
rpoC765499c.2130C>G1.000
rpoC765892c.2523T>C0.900
rpoC765961c.2592G>A0.909
rpoC765967c.2598C>T0.909
rpoC765979c.2610C>G0.900
rpoC765994c.2625A>T0.900
rpoC766009c.2640G>C0.909
rpoC766010c.2641T>A0.909
rpoC766027c.2658G>T0.909
rpoC766348c.2979A>G1.000
rpoC766351c.2982C>G1.000
rpoC766363c.2994G>C1.000
rpoC766366c.2997C>G1.000
rpoC766447c.3078T>C1.000
rpoC766462c.3093G>C1.000
rpoC766484p.Val1039Ile1.000
rpoC766609p.Ile1080Met1.000
rpoC766618c.3249G>T0.900
rpoC766624c.3255G>C1.000
rpoC766645c.3276A>G1.000
rpoC766651c.3282T>C1.000
rpoC766657c.3288A>G1.000
rpoC766667p.Ser1100Ala1.000
rpoC766672c.3303T>C1.000
rpoC766690c.3321G>T1.000
rpoC766714c.3345G>C1.000
rpoC766726c.3357T>C1.000
rpoC766738c.3369G>T1.000
rpoC766750c.3381C>G1.000
rpoC766753c.3384C>T1.000
rpoC766765c.3396A>C1.000
rpoC766774c.3405T>C1.000
rpoC766801c.3432C>G0.900
rpoC766804c.3435A>G0.917
rpoC766843c.3474T>C0.917
rpoC766846c.3477C>T0.923
rpoC766864c.3495G>C0.929
rpoC766894c.3525T>C0.900
rpoC766895c.3526T>C0.889
rpoC767059c.3690T>G1.000
rpoC767062c.3693C>A1.000
rpoC767098c.3729T>C1.000
rpoC767119c.3750A>G1.000
rpoC767134c.3765C>A1.000
rpoC767167c.3798C>G1.000
rpoC767173c.3804C>G1.000
rpoC767180p.Ala1271Gln1.000
rpoC767191c.3822C>G1.000
rpoC767212c.3843G>C0.900
rpoC767221c.3852C>G0.917
rpoC767233c.3864T>C0.909
rpsL781715c.156T>C1.000
rpsL781718c.159C>T1.000
rpsL781721c.162C>T1.000
rpsL781728c.169T>C1.000
rpsL781742c.183C>T1.000
rpsL781754c.195G>C1.000
rpsL781763c.204C>G1.000
embR1416330p.Val340Ile0.917
embR1416340c.1008G>C0.929
embR1416343c.1005C>G0.929
embR1416379c.969G>C0.929
embR1416388c.960T>C0.917
rrs1471866r.21c>t1.000
rrs1471918r.73a>t1.000
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471934r.89a>g1.000
rrs1471938r.93t>a1.000
rrs1471970r.125g>a1.000
rrs1471984r.139t>a1.000
rrs1472019r.174g>a1.000
rrs1472030r.185g>a1.000
rrs1472032r.187g>a1.000
rrs1472034r.189t>c1.000
rrs1472042r.197t>c0.938
rrs1472061r.216a>t0.950
rrs1472075r.230a>g0.952
rrs1472108r.263c>t0.955
rrs1472113r.268t>c0.917
rrs1472225r.380c>a1.000
rrs1472314r.469a>g1.000
rrs1472315r.470t>c1.000
rrs1472489r.644a>t0.955
rrs1472755r.910g>a1.000
rrs1472969r.1124a>g0.952
rrs1472970r.1125c>g0.947
rrs1472977r.1132g>c0.955
rrs1472978r.1133t>c0.955
rrs1473120r.1275c>ct0.828
rrs1473123r.1278a>t1.000
rrs1473288r.1443c>ct0.864
rrs1473290r.1445c>t0.950
rrl1473653c.-5T>A1.000
rrl1473758r.101g>t1.000
rrl1473806r.149c>t0.963
rrl1473813r.156c>t0.963
rrl1473815r.158t>c0.964
rrl1473839r.182g>t1.000
rrl1473876r.219g>a1.000
rrl1473899r.242a>t1.000
rrl1473923r.266c>a1.000
rrl1473937r.280c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1474090r.433c>t0.909
rrl1474093r.436g>a0.900
rrl1474103r.446a>t0.900
rrl1474127r.470g>a1.000
rrl1474139r.482c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474266r.609t>c0.957
rrl1474290r.633ttttcctctccggagg>t0.950
rrl1474306r.649a>c0.909
rrl1474308r.651g>t0.909
rrl1474310r.653t>g0.929
rrl1474362r.705a>g1.000
rrl1474447r.790g>a0.955
rrl1474639r.982g>a0.913
rrl1474716r.1059a>c0.917
rrl1474794r.1137c>a0.929
rrl1474812r.1155g>a0.964
rrl1474831r.1174a>g0.964
rrl1474957r.1300c>t0.818
rrl1475006r.1349a>g1.000
rrl1475007r.1350c>t1.000
rrl1475013r.1356g>a1.000
rrl1475018r.1361g>t1.000
rrl1475019r.1362t>a0.947
rrl1475028r.1371g>a1.000
rrl1475061r.1404c>a1.000
rrl1475062r.1405a>t1.000
rrl1475202r.1545g>c1.000
rrl1475213r.1556c>t1.000
rrl1475315r.1658a>c0.941
rrl1475355r.1698c>t0.960
rrl1475369r.1712g>c0.950
rrl1475402r.1745c>t1.000
rrl1475429r.1772g>a1.000
rrl1475479r.1822c>t1.000
rrl1475480r.1823a>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475573r.1916g>a1.000
rrl1475599r.1942a>g1.000
rrl1475604r.1947a>c1.000
rrl1475606r.1949t>c1.000
rrl1475619r.1962c>t1.000
rrl1475622r.1965g>t1.000
rrl1475635r.1978g>a1.000
rrl1475637r.1980t>g1.000
rrl1475659r.2002g>a1.000
rrl1475760r.2103c>t0.875
rrl1475763r.2106c>t0.875
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1476131r.2474c>t1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476580r.2923g>a1.000
rrl1476597r.2940g>a1.000
rrl1476608r.2951c>t1.000
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
rrl1476689r.3032a>t1.000
rrl1476692r.3035t>a1.000
rrl1476695r.3038t>a1.000
rrl1476710r.3053c>a0.913
rrl1476720r.3063g>t0.882
rrl1476723r.3066t>a0.875
rrl1476725r.3068c>t0.867
rrl1476726r.3069a>g0.875
rrl1476732r.3075t>c0.875
inhA1674870c.669T>C1.000
rpsA1833811c.270G>T1.000
rpsA1833817c.276C>G1.000
rpsA1833820c.279G>A1.000
rpsA1833856c.315A>G1.000
rpsA1833859c.318C>T1.000
rpsA1833874c.333T>C1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833928c.387G>C1.000
rpsA1833979c.438T>C1.000
rpsA1833988c.447C>G1.000
rpsA1834000c.459G>C1.000
rpsA1834012c.471G>C1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834051c.510G>A1.000
rpsA1834249c.708T>C0.900
rpsA1834261c.720A>G0.929
rpsA1834264c.723G>C0.929
rpsA1834297c.756C>G1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834372c.831G>A1.000
rpsA1834378c.837T>C1.000
rpsA1834396c.855G>C1.000
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>T1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>C1.000
rpsA1834459c.918G>C1.000
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834606c.1065C>T1.000
rpsA1834609c.1068T>C1.000
rpsA1834612c.1071G>T1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654c.1113G>A1.000
rpsA1834666c.1125G>C1.000
rpsA1834669c.1128G>C1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
kasA2518219c.105T>C0.923
kasA2518220c.106C>T0.923
kasA2518234c.120G>A0.923
kasA2518247p.Ala45Thr0.923
kasA2518261p.Glu49Asp0.923
kasA2518268p.Thr52Ser0.909
kasA2518273c.159G>A0.909
folC2747104c.495G>A0.909
folC2747110c.489A>G0.909
folC2747113c.486G>C0.909
thyX3067765p.Leu61Ile1.000
thyX3067781c.165G>C1.000
thyX3067789p.Lys53Arg1.000
thyX3067790c.156G>C1.000
thyX3067849p.Pro33Ser0.917
thyX3067849r.97gt>g1.000
thyX3067850c.96T>G1.000
thyX3067853c.93G>C1.000
thyX3067874c.72G>C1.000
fbiA3640302c.-241T>A1.000
fbiA3640303c.-240TA>T1.000
fbiA3640305c.-238A>G1.000
fbiA3640347c.-196A>G1.000
fbiA3640365c.-178C>G1.000
embC4240766c.904C>A0.917
embC4240780c.918T>C0.846
embC4240783c.921G>C0.833
embC4240789c.927T>C0.833
embC4240819c.957A>G0.917
embC4240831c.969T>G0.917
embC4241119c.1257C>G1.000
embB4247434c.921C>G0.900
embB4247437c.924A>C0.900
embB4247491c.978G>C0.929
embB4247497c.984T>C0.929
embB4247512c.999T>C0.900
embB4247989c.1476G>C1.000
embB4248064c.1551G>C1.000
embB4248070c.1557T>C1.000
embB4248097c.1584C>G1.000
embB4248098p.Ile529Phe1.000
embB4248106c.1593C>G1.000
embB4248130c.1617G>C1.000
embB4248133c.1620C>G1.000
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248149p.Thr546Ala1.000
embB4248157c.1644A>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.

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;