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: 5cc54dd975314
Sample: 5cc54dd975314

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Summary
ID: 5cc54dd975314
Date: Sun Apr 28 07:54:26 2019
Strain: lineageBOV;lineage4.3;lineage4.3.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineageBOVM. bovisBOV 1;BOV 2None
lineage4.3.1Euro-American (LAM)LAM9None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7547c.246C>T1.000
gyrA8294c.993T>C1.000
gyrA8324c.1023T>C1.000
gyrA8339c.1038A>C1.000
gyrA8340p.Ala347Ser1.000
gyrA8366c.1065G>C1.000
gyrA8378c.1077C>T1.000
gyrA8382p.Leu361Met1.000
rpoB760235c.429T>C1.000
rpoB760283c.477G>C1.000
rpoB762929c.3123G>C1.000
rpoB762962c.3156C>T1.000
rpoB763142c.3336C>G0.900
rpoC763396c.27A>G1.000
rpoC763408c.39T>C1.000
rpoC763411c.42T>G1.000
rpoC763414c.45T>G1.000
rpoC763430c.61A>C1.000
rpoC763444c.75T>C1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763657c.288G>A1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>T1.000
rpoC763669c.300C>G1.000
rpoC764134c.765C>G1.000
rpoC764365c.996C>T1.000
rpoC764387c.1018T>C1.000
rpoC764827c.1458G>C1.000
rpoC764863c.1494G>C1.000
rpoC764869c.1500C>G1.000
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764905c.1536C>T1.000
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln1.000
rpoC764923c.1554A>G1.000
rpoC764948c.1579T>C1.000
rpoC764962c.1593G>C1.000
rpoC764968c.1599T>C1.000
rpoC764995c.1626C>G1.000
rpoC765007c.1638T>G1.000
rpoC765008c.1639T>C1.000
rpoC765019c.1650A>G1.000
rpoC765034c.1665T>C1.000
rpoC765076c.1707A>C1.000
rpoC765079c.1710T>G1.000
rpoC765662c.2293T>C1.000
rpoC765673p.Asp768Glu1.000
rpoC765700c.2331T>C1.000
rpoC765718p.Asp783Glu1.000
rpoC765850c.2481G>C0.909
rpoC765904c.2535C>G1.000
rpoC765967c.2598C>T1.000
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766357c.2988C>T1.000
rpoC766363c.2994G>C1.000
rpoC766366c.2997C>G1.000
rpoC766390c.3021C>T1.000
rpoC766690c.3321G>C1.000
rpoC766702c.3333G>C1.000
rpoC766708c.3339A>G1.000
rpoC766711c.3342C>T1.000
rpoC767059c.3690T>C1.000
rpoC767098c.3729T>C1.000
rpoC767104c.3735C>G1.000
rpoC767105p.Asn1246Gln1.000
rpoC767113c.3744G>C1.000
rpoC767119c.3750A>G1.000
rpoC767152c.3783T>C1.000
rpoC767158c.3789T>C1.000
rpoC767167c.3798C>G1.000
rpoC767191c.3822C>G1.000
rpoC767206c.3837C>G1.000
rpoC767209c.3840T>C1.000
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rrs1471896r.51t>c0.802
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471936r.91a>g1.000
rrs1471985r.140t>c1.000
rrs1471986r.141c>t1.000
rrs1471996r.151c>t1.000
rrs1472029r.184c>t1.000
rrs1472041r.196c>t1.000
rrs1472042r.197t>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t1.000
rrs1472127r.282c>t0.283
rrs1472128r.283g>c0.283
rrs1472129r.284g>a0.200
rrs1472138r.293c>t0.367
rrs1472147r.302g>a0.442
rrs1472150r.305t>a0.479
rrs1472151r.306c>a0.479
rrs1472172r.327t>c0.579
rrs1472327r.482g>a1.000
rrs1472328r.483g>c1.000
rrs1472378r.533g>t0.552
rrs1472379r.534t>g0.585
rrs1472400r.555c>t0.576
rrs1472415r.570t>g0.576
rrs1472438r.593t>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472456r.611t>c1.000
rrs1472464r.619a>g1.000
rrs1472489r.644a>g1.000
rrs1472498r.653c>t1.000
rrs1472683r.838t>tta0.939
rrs1472697r.852t>g0.200
rrs1472700r.855c>t0.206
rrs1472708r.863t>a0.735
rrs1472742r.897c>t0.787
rrs1472744r.899a>g0.783
rrs1472781r.936c>t0.781
rrs1472786r.941c>t0.750
rrs1472793r.948a>t0.752
rrs1472803r.958t>c0.716
rrs1472824r.979t>a0.194
rrs1472847r.1002g>c0.955
rrs1472848r.1003t>g0.955
rrs1472849r.1004c>g0.955
rrs1472858r.1013g>t0.957
rrs1472859r.1014g>c0.957
rrs1472860r.1015c>g0.957
rrs1472953r.1108g>a0.587
rrs1472956r.1111t>c0.560
rrs1472957r.1112c>t0.567
rrs1472969r.1124a>g0.255
rrs1472970r.1125c>a0.222
rrs1472973r.1128a>t0.768
rrs1472975r.1130t>a0.218
rrs1472977r.1132g>t0.222
rrs1472978r.1133t>c0.241
rrs1472982r.1137g>a0.222
rrs1472987r.1142g>a0.211
rrs1472990r.1145a>g0.211
rrs1473001r.1156g>c0.218
rrs1473002r.1157g>a0.226
rrs1473004r.1159t>a0.226
rrs1473008r.1163c>t0.226
rrs1473009r.1164t>g0.226
rrs1473020r.1175t>c0.207
rrs1473056r.1211a>t0.216
rrs1473100r.1255g>c1.000
rrs1473104r.1259c>t1.000
rrs1473109r.1264t>g1.000
rrs1473111r.1266a>t1.000
rrs1473123r.1278a>t0.968
rrs1473145r.1300c>t0.222
rrs1473147r.1302g>c0.521
rrs1473148r.1303g>a0.521
rrs1473150r.1305t>g0.534
rrs1473161r.1316a>c0.520
rrs1473163r.1318c>t0.520
rrs1473164r.1319c>g0.519
rrs1473166r.1321g>a0.434
rrs1473177r.1332g>a0.551
rrs1473199r.1354ca>c0.594
rrs1473202r.1357c>t0.576
rrs1473248r.1403g>a0.174
rrs1473249r.1404t>c0.178
rrs1473252r.1407t>c0.170
rrs1473259r.1414c>t0.167
rrs1473262r.1417t>a0.163
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473301r.1456t>c1.000
rrs1473352r.1507c>t0.594
rrl1473384c.-274A>G0.448
rrl1473668r.11c>t1.000
rrl1473770r.113t>g1.000
rrl1473788r.131a>g1.000
rrl1473839r.182g>t1.000
rrl1473877r.220g>a1.000
rrl1473887r.230t>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1474016r.359c>g1.000
rrl1474026r.369c>t1.000
rrl1474083r.426c>t1.000
rrl1474089r.432c>t1.000
rrl1474093r.436g>a1.000
rrl1474116r.459g>a1.000
rrl1474127r.470g>a1.000
rrl1474139r.482c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g0.962
rrl1474181r.524c>t1.000
rrl1474201r.544t>c0.952
rrl1474202r.545t>g0.952
rrl1474249r.592g>t1.000
rrl1474263r.606g>a1.000
rrl1474310r.653t>g1.000
rrl1474350r.693g>c0.967
rrl1474351r.694g>c1.000
rrl1474353r.696a>g1.000
rrl1474356r.699t>c1.000
rrl1474362r.705a>g1.000
rrl1474374r.717t>g1.000
rrl1474452r.795c>g1.000
rrl1474552r.895c>t0.923
rrl1474632r.975g>t0.929
rrl1474636r.979a>t0.857
rrl1474638r.981c>a1.000
rrl1474639r.982g>c1.000
rrl1474715r.1058ta>t1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1475031r.1374g>t0.905
rrl1475037r.1380t>c0.952
rrl1475061r.1404c>t1.000
rrl1475062r.1405a>g1.000
rrl1475120r.1463g>t0.978
rrl1475206r.1549c>t1.000
rrl1475209r.1552g>c1.000
rrl1475213r.1556c>t1.000
rrl1475291r.1634a>c1.000
rrl1475297r.1640c>t1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t0.955
rrl1475363r.1706c>t0.933
rrl1475375r.1718g>a0.923
rrl1475378r.1721a>t0.923
rrl1475379r.1722g>c0.923
rrl1475380r.1723c>a0.923
rrl1475482r.1825a>g1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475544r.1887a>t1.000
rrl1475545r.1888t>g1.000
rrl1475573r.1916g>a1.000
rrl1475659r.2002g>a1.000
rrl1475753r.2096c>g0.955
rrl1475762r.2105g>t0.947
rrl1475763r.2106c>t1.000
rrl1475764r.2107a>c0.947
rrl1475765r.2108a>g0.947
rrl1475775r.2118g>t0.958
rrl1475783r.2126t>g0.537
rrl1475803r.2146t>c0.574
rrl1475804r.2147g>c0.581
rrl1475816r.2159c>g0.594
rrl1475817r.2160a>g0.594
rrl1475858r.2201t>c0.541
rrl1475866r.2209t>a0.482
rrl1475869r.2212c>t0.455
rrl1475916r.2259c>t1.000
rrl1475975r.2318c>t0.967
rrl1475977r.2320a>g0.960
rrl1475995r.2338g>a0.960
rrl1475997r.2340a>g0.960
rrl1476033r.2376t>c0.947
rrl1476034r.2377c>g0.947
rrl1476035r.2378g>c0.947
rrl1476044r.2387t>g0.950
rrl1476045r.2388g>t0.950
rrl1476049r.2392c>t0.950
rrl1476086r.2429g>a0.944
rrl1476088r.2431a>c1.000
rrl1476095r.2438c>t1.000
rrl1476103r.2446c>a1.000
rrl1476108r.2451t>g1.000
rrl1476110r.2453g>t1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g0.833
rrl1476225r.2568t>g0.167
rrl1476229r.2572c>g0.258
rrl1476245r.2588c>t0.538
rrl1476246r.2589g>a0.519
rrl1476251r.2594t>g0.483
rrl1476252r.2595t>g0.517
rrl1476256r.2599a>g0.467
rrl1476260r.2603a>g0.424
rrl1476262r.2605g>a0.559
rrl1476280r.2623a>c0.538
rrl1476281r.2624t>c0.475
rrl1476293r.2636c>t0.488
rrl1476294r.2637a>g0.488
rrl1476295r.2638c>g0.488
rrl1476296r.2639c>t0.488
rrl1476297r.2640c>a0.488
rrl1476311r.2654g>c0.567
rrl1476312r.2655t>c0.567
rrl1476313r.2656g>a0.567
rrl1476332r.2675g>c0.671
rrl1476338r.2681c>t0.688
rrl1476353r.2696g>a0.705
rrl1476358r.2701t>c0.674
rrl1476359r.2702c>t0.663
rrl1476382r.2725a>g0.696
rrl1476383r.2726t>a0.708
rrl1476408r.2751g>a0.736
rrl1476411r.2754g>a0.738
rrl1476425r.2768g>a0.761
rrl1476428r.2771c>t0.766
rrl1476463r.2806c>t0.779
rrl1476466r.2809c>t0.769
rrl1476470r.2813c>t0.757
rrl1476481r.2824t>c0.700
rrl1476506r.2849t>c0.580
rrl1476529r.2872a>t0.941
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>g1.000
rrl1476616r.2959a>g1.000
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c1.000
rrl1476665r.3008t>a1.000
rrl1476674r.3017t>c1.000
rrl1476679r.3022t>a1.000
rrl1476690r.3033c>t1.000
rrl1476692r.3035t>a1.000
rrl1476693r.3036g>a1.000
rrl1476716r.3059a>c1.000
rrl1476723r.3066t>a1.000
rpsA1833589c.48A>C1.000
rpsA1833595c.54T>G1.000
rpsA1833596p.Ser19Gly0.900
rpsA1833604c.63C>T1.000
rpsA1833616c.75A>C1.000
rpsA1833619c.78A>C0.917
rpsA1833778c.237C>G1.000
rpsA1833781c.240T>G1.000
rpsA1833802c.261A>G1.000
rpsA1833805c.264C>T1.000
rpsA1833811c.270G>C1.000
rpsA1833814c.273C>G1.000
rpsA1833835c.294C>T1.000
rpsA1833874c.333T>C1.000
rpsA1833886c.345C>G1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833949c.408T>C0.909
rpsA1833976c.435C>T1.000
rpsA1833979c.438T>C1.000
rpsA1834042p.Lys167Asn1.000
rpsA1834051c.510G>A1.000
rpsA1834102c.561T>C1.000
rpsA1834690c.1149T>C1.000
thyX3067814c.132A>G1.000
thyX3067850c.96T>C1.000
thyX3067869p.Thr26Ser1.000

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
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