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: 5cc55b406af65
Sample: 5cc55b406af65

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Summary
ID: 5cc55b406af65
Date: Sun Apr 28 08:56:06 2019
Strain: lineage2;lineage4.3.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage4.3.1Euro-American (LAM)LAM9None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6763c.1524G>C1.000
gyrB6775c.1536G>C1.000
gyrB6793c.1554T>C1.000
gyrB6797p.Gly520Ser1.000
gyrB6808c.1569C>G1.000
gyrA7463c.162G>C1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>T1.000
gyrA7496c.195C>T1.000
gyrA7499c.198G>T1.000
gyrA7523c.222C>G1.000
gyrA7526c.225G>C1.000
gyrA7532c.231T>G0.950
gyrA7541c.240C>G1.000
gyrA7547c.246C>T1.000
gyrA7585p.Ser95Thr1.000
gyrA7592c.291G>C1.000
gyrA7607c.306C>G1.000
gyrA7760c.459C>T1.000
gyrA7763c.462T>G1.000
gyrA7790c.489G>C1.000
gyrA7793c.492G>C1.000
gyrA7814c.513C>G1.000
gyrA7835c.534A>G1.000
gyrA7841c.540C>T1.000
gyrA7859c.558A>C1.000
gyrA7865c.564T>C1.000
gyrA8867c.1566A>G1.000
gyrA8873c.1572A>T1.000
gyrA8897c.1596T>C1.000
gyrA8903c.1602T>C1.000
gyrA8915c.1614A>G1.000
gyrA9296c.1995T>C1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760244c.438G>C1.000
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760340c.534G>T1.000
rpoB760357p.Thr184Ser1.000
rpoB760361c.555T>C1.000
rpoB760376p.Asp190Glu1.000
rpoB760406c.600G>C1.000
rpoB760407p.Ser201Gly1.000
rpoB760661c.855A>C1.000
rpoB761015c.1209G>C1.000
rpoB761051c.1245G>T1.000
rpoB761054c.1248G>C1.000
rpoB761057c.1251G>C1.000
rpoB761060c.1254C>G1.000
rpoB761063c.1257C>G1.000
rpoB761180c.1374A>C1.000
rpoB761189c.1383T>C1.000
rpoB761195c.1389G>C1.000
rpoB761234c.1428G>C1.000
rpoB761249c.1443A>G1.000
rpoB761261c.1455G>T1.000
rpoB761264c.1458C>G1.000
rpoB761300c.1494G>C1.000
rpoB761318c.1512G>C1.000
rpoB761327c.1521A>G1.000
rpoB761345c.1539G>C1.000
rpoB761346p.Val514Ile1.000
rpoB761354c.1548C>T1.000
rpoB761360c.1554T>C1.000
rpoB761999c.2193G>C1.000
rpoB762002c.2196C>G1.000
rpoB762038c.2232C>T1.000
rpoB762047c.2241G>A1.000
rpoB762053c.2247T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762149c.2343G>C1.000
rpoB762158c.2352G>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762209c.2403C>A0.200
rpoB762245c.2439G>C1.000
rpoB762284c.2478G>T0.900
rpoB762878p.Ile1024Met1.000
rpoB762879p.Met1025Leu1.000
rpoB762929c.3123G>C1.000
rpoB762959c.3153G>C1.000
rpoB762962c.3156C>T1.000
rpoB762989c.3183G>A1.000
rpoB762995c.3189G>T1.000
rpoB763004c.3198G>A1.000
rpoB763007c.3201C>T1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>C1.000
rpoB763053c.3247T>C1.000
rpoB763070c.3264T>C1.000
rpoB763085c.3279C>G1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763576c.207C>G1.000
rpoC763594c.225C>T1.000
rpoC763621c.252C>T1.000
rpoC763633c.264T>C1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>A1.000
rpoC763675c.306C>G1.000
rpoC763741c.372C>T1.000
rpoC763747c.378G>A1.000
rpoC764131c.762T>C1.000
rpoC764153p.Gln262Lys1.000
rpoC764161c.792G>C1.000
rpoC764701c.1332C>G1.000
rpoC764713c.1344G>T1.000
rpoC764734c.1365C>T1.000
rpoC764746c.1377G>T1.000
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G1.000
rpoC764764c.1395T>C1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764827c.1458G>C1.000
rpoC764858c.1489T>C1.000
rpoC764869c.1500C>T1.000
rpoC764875c.1506C>T1.000
rpoC764878c.1509C>G1.000
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764911c.1542A>G0.933
rpoC764912p.Met515Gln1.000
rpoC764935c.1566T>C1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765871c.2502T>C1.000
rpoC765875p.Val836Ile1.000
rpoC765886c.2517C>G1.000
rpoC765904c.2535C>G1.000
rpoC765934c.2565C>T1.000
rpoC765940c.2571A>T1.000
rpoC765946c.2577C>T1.000
rpoC765947c.2578T>C1.000
rpoC765952c.2583G>C1.000
rpoC767068c.3699G>C1.000
rpsL781760c.201T>C1.000
rpsL781766c.207C>T1.000
rpsL781772c.213C>T1.000
rpsL781793c.234G>C1.000
rpsL781892c.333A>G1.000
rrs1471896r.51t>c0.534
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471934r.89a>g1.000
rrs1471986r.141c>t1.000
rrs1472019r.174g>a1.000
rrs1472028r.183a>g1.000
rrs1472031r.186g>c1.000
rrs1472032r.187g>t1.000
rrs1472033r.188a>c1.000
rrs1472035r.190g>t1.000
rrs1472040r.195t>g1.000
rrs1472041r.196c>g1.000
rrs1472042r.197t>g1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472127r.282c>t0.157
rrs1472128r.283g>c0.160
rrs1472138r.293c>a0.176
rrs1472147r.302g>t0.170
rrs1472150r.305t>a1.000
rrs1472151r.306c>a0.176
rrs1472160r.315c>t0.176
rrs1472172r.327t>c0.205
rrs1472207r.362a>g0.163
rrs1472251r.406g>a1.000
rrs1472337r.492c>g0.775
rrs1472338r.493a>t0.225
rrs1472344r.499c>t0.273
rrs1472379r.534t>a0.226
rrs1472380r.535g>c0.774
rrs1472396r.551a>t0.233
rrs1472405r.560c>t0.222
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
rrs1472742r.897c>t0.259
rrs1472744r.899a>g0.271
rrs1472779r.934g>a0.242
rrs1472781r.936c>t0.242
rrs1472786r.941c>t0.239
rrs1472793r.948a>t0.239
rrs1472803r.958t>a0.239
rrs1472847r.1002g>c1.000
rrs1472848r.1003t>a1.000
rrs1472849r.1004c>g1.000
rrs1472858r.1013g>t1.000
rrs1472859r.1014g>t1.000
rrs1472860r.1015c>g1.000
rrs1472895r.1050c>t0.286
rrs1472973r.1128a>t1.000
rrs1473104r.1259c>t1.000
rrs1473110r.1265t>g1.000
rrs1473111r.1266a>g1.000
rrs1473120r.1275c>ct0.912
rrs1473123r.1278a>c1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>gt1.000
rrs1473301r.1456t>c1.000
rrs1473352r.1507c>t0.233
rrl1473668r.11c>t1.000
rrl1473696r.39t>c1.000
rrl1473697r.40c>t1.000
rrl1473699r.42a>g1.000
rrl1473717r.60g>t1.000
rrl1473746r.89t>c1.000
rrl1473758r.101g>t1.000
rrl1473770r.113t>g1.000
rrl1473806r.149c>t1.000
rrl1473813r.156c>t1.000
rrl1473814r.157a>c1.000
rrl1473815r.158t>a1.000
rrl1473823r.166t>c1.000
rrl1473829r.172g>t0.905
rrl1473830r.173t>g0.905
rrl1473831r.174g>t0.913
rrl1473876r.219g>a1.000
rrl1473884r.227c>ca0.941
rrl1473887r.230t>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1473922r.265a>g1.000
rrl1473923r.266c>g1.000
rrl1473924r.267a>at1.000
rrl1473935r.278c>t1.000
rrl1473937r.280c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1474135r.478g>a1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g1.000
rrl1474181r.524c>t1.000
rrl1474183r.526t>c0.923
rrl1474185r.528g>a1.000
rrl1474186r.529a>g0.963
rrl1474249r.592g>t1.000
rrl1474266r.609t>c1.000
rrl1474269r.612c>t1.000
rrl1474289r.632c>t1.000
rrl1474292r.635t>g1.000
rrl1474294r.637cctctccggagga>c1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474362r.705a>g1.000
rrl1474446r.789c>t1.000
rrl1474626r.969t>c1.000
rrl1474627r.970g>a1.000
rrl1474629r.972g>a1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t1.000
rrl1474637r.980c>t1.000
rrl1474638r.981c>g1.000
rrl1474639r.982g>t1.000
rrl1474640r.983c>t1.000
rrl1474673r.1016t>c1.000
rrl1474676r.1019t>a1.000
rrl1474677r.1020a>g1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1475031r.1374g>t1.000
rrl1475061r.1404c>a1.000
rrl1475062r.1405a>t1.000
rrl1475120r.1463g>t1.000
rrl1475315r.1658a>t1.000
rrl1475353r.1696a>t1.000
rrl1475354r.1697a>g1.000
rrl1475355r.1698c>t1.000
rrl1475363r.1706c>t1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>t1.000
rrl1475452r.1795c>a1.000
rrl1475479r.1822c>g1.000
rrl1475483r.1826c>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475544r.1887a>t1.000
rrl1475545r.1888t>g1.000
rrl1475659r.2002g>a1.000
rrl1475753r.2096c>t1.000
rrl1475762r.2105g>t1.000
rrl1475763r.2106c>t1.000
rrl1475764r.2107a>c1.000
rrl1475765r.2108a>g1.000
rrl1475775r.2118g>a1.000
rrl1475783r.2126t>g0.326
rrl1475803r.2146t>c0.346
rrl1475804r.2147g>c0.353
rrl1475816r.2159c>g0.311
rrl1475817r.2160a>g0.297
rrl1475858r.2201t>c0.316
rrl1475869r.2212c>t0.271
rrl1475988r.2331a>g1.000
rrl1475991r.2334t>c1.000
rrl1475995r.2338g>a1.000
rrl1476014r.2357g>a0.368
rrl1476044r.2387t>g1.000
rrl1476045r.2388g>t1.000
rrl1476049r.2392c>t1.000
rrl1476088r.2431a>c1.000
rrl1476099r.2442a>g1.000
rrl1476103r.2446c>g1.000
rrl1476105r.2448g>a1.000
rrl1476106r.2449a>t1.000
rrl1476110r.2453g>c1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476160r.2503t>c1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t0.971
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>g1.000
rrl1476256r.2599a>t1.000
rrl1476260r.2603a>g1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476332r.2675g>c0.207
rrl1476338r.2681c>t0.269
rrl1476358r.2701t>c0.300
rrl1476372r.2715t>c0.268
rrl1476382r.2725a>g0.282
rrl1476383r.2726t>a0.282
rrl1476408r.2751g>a0.263
rrl1476411r.2754g>a0.275
rrl1476425r.2768g>t0.211
rrl1476427r.2770g>t0.211
rrl1476428r.2771c>t0.216
rrl1476429r.2772a>c0.265
rrl1476443r.2786g>c0.245
rrl1476455r.2798c>g0.204
rrl1476463r.2806c>t0.204
rrl1476466r.2809c>t0.208
rrl1476481r.2824t>c0.200
rrl1476506r.2849t>c0.173
rrl1476529r.2872a>g1.000
rrl1476540r.2883c>t1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c1.000
rrl1476665r.3008t>c1.000
rrl1476674r.3017t>c1.000
rrl1476679r.3022t>c1.000
inhA1674450c.249G>T1.000
inhA1674471c.270G>C1.000
inhA1674480c.279T>C1.000
rpsA1833685c.144G>T1.000
rpsA1834097c.556T>A1.000
rpsA1834102c.561T>C1.000
rpsA1834213c.672G>C1.000
rpsA1834234c.693G>C1.000
rpsA1834240c.699T>C1.000
rpsA1834249c.708T>C1.000
rpsA1834259c.718C>T1.000
rpsA1834264c.723G>C1.000
rpsA1834279c.738C>T1.000
rpsA1834297c.756C>T1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834387c.846C>T1.000
rpsA1834396c.855G>T1.000
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>C1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834468c.927A>G1.000
rpsA1834483c.942G>A1.000
rpsA1834489c.948T>C1.000
rpsA1834513c.972C>G1.000
rpsA1834520p.Ala327Ser1.000
rpsA1834528c.987T>C1.000
rpsA1834540c.999G>C1.000
rpsA1834543c.1002C>G1.000
rpsA1834546c.1005T>C1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G1.000
embC4240783c.921G>C1.000
embC4240789c.927T>C1.000
embC4240819c.957A>C1.000
embC4240825c.963G>A1.000
embC4240828c.966G>C1.000
embC4240831c.969T>G1.000
embB4247524c.1011G>C1.000
embB4247527c.1014G>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
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