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: 5cc554f46734a
Sample: 5cc554f46734a

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Summary
ID: 5cc554f46734a
Date: Sun Apr 28 08:27:43 2019
Strain: lineage4.3;lineage4.2.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineageBOV AFRI???

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6100c.861G>C1.000
gyrB6115c.876A>G1.000
gyrB6123p.Ala295Gly1.000
gyrB6127c.888G>T1.000
gyrB6130c.891T>C1.000
gyrB6148c.909C>G1.000
gyrA7457c.156T>C1.000
gyrA7472c.171T>C1.000
gyrA7475c.174A>G1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>G1.000
gyrA7502c.201C>T1.000
gyrA7506p.Ser69Gly1.000
gyrA7526c.225G>C1.000
gyrA7532c.231T>C1.000
gyrA7569p.Ala90Ser1.000
gyrA7585p.Ser95Thr1.000
gyrA8987c.1686C>G1.000
gyrA8996c.1695T>C1.000
gyrA8998p.Leu566Trp1.000
gyrA9017c.1716C>G1.000
gyrA9023c.1722A>C1.000
gyrA9029c.1728T>G1.000
gyrA9051c.1750T>C1.000
gyrA9056c.1755C>G1.000
rpoB761015c.1209G>C1.000
rpoB761021c.1215G>C1.000
rpoB761027c.1221A>G1.000
rpoB761037c.1231T>C1.000
rpoB761066c.1260G>C1.000
rpoB762911c.3105C>T1.000
rpoB762929c.3123G>T1.000
rpoB762989c.3183G>C1.000
rpoB762995c.3189G>T1.000
rpoB763058c.3252C>G1.000
rpoB763070c.3264T>C1.000
rpoB763094c.3288G>C1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>C1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763639c.270G>A1.000
rpoC763660c.291T>G1.000
rpoC763669c.300C>G1.000
rpoC764344c.975C>T1.000
rpoC764365c.996C>T1.000
rpoC764387c.1018T>C1.000
rpoC764650c.1281G>T1.000
rpoC764665c.1296C>G1.000
rpoC765047c.1678T>C1.000
rpoC765052c.1683C>T1.000
rpoC765421c.2052C>G1.000
rpoC765453p.Ala695Val1.000
rpoC765508c.2139C>G1.000
rpoC765628c.2259G>C1.000
rpoC765640c.2271A>G1.000
rpoC765751c.2382C>G1.000
rpoC765753p.Asp795Ala1.000
rpoC765787c.2418C>T1.000
rpoC765793c.2424C>G1.000
rpoC765796c.2427C>T1.000
rpoC765811c.2442T>C1.000
rpoC765814c.2445A>G1.000
rpoC765826c.2457T>C1.000
rpoC765961c.2592G>C1.000
rpoC765967c.2598C>T1.000
rpoC766345c.2976T>C0.917
rpoC766348c.2979A>G0.917
rpoC766357c.2988C>T0.909
rpoC766363c.2994G>C0.909
rpoC766366c.2997C>G0.909
rpoC766384c.3015A>G0.917
rpoC766390c.3021C>T0.929
rpoC766804c.3435A>G1.000
rpoC767119c.3750A>G1.000
rpoC767158c.3789T>C1.000
rpoC767167c.3798C>G1.000
rpsL781658c.99A>C1.000
rpsL781709c.150G>C1.000
rpsL781808c.249C>T1.000
rpsL781811c.252C>T1.000
rpsL781832c.273T>G1.000
rrs1471985r.140t>c0.545
rrs1471986r.141c>t1.000
rrs1472029r.184c>t1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t1.000
rrs1472327r.482g>a1.000
rrs1472328r.483g>c1.000
rrs1472438r.593t>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
rrs1472489r.644a>g1.000
rrs1472498r.653c>t1.000
rrs1472598r.753a>c0.132
rrs1472616r.771g>a0.128
rrs1472683r.838t>tta0.903
rrs1472847r.1002g>c1.000
rrs1472848r.1003t>g1.000
rrs1472849r.1004c>g1.000
rrs1472858r.1013g>t1.000
rrs1472859r.1014g>c1.000
rrs1472860r.1015c>g1.000
rrs1472973r.1128a>g1.000
rrs1473104r.1259c>t1.000
rrs1473111r.1266a>t1.000
rrs1473123r.1278a>t1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473301r.1456t>c1.000
rrl1473668r.11c>g1.000
rrl1473770r.113t>g1.000
rrl1473788r.131a>g1.000
rrl1473793r.136g>c1.000
rrl1473839r.182g>t1.000
rrl1473877r.220g>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1474083r.426c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g0.963
rrl1474181r.524c>t0.957
rrl1474201r.544t>c0.952
rrl1474202r.545t>g0.952
rrl1474263r.606g>a0.952
rrl1474290r.633t>g1.000
rrl1474350r.693g>c1.000
rrl1474351r.694g>c1.000
rrl1474353r.696a>g1.000
rrl1474356r.699t>c1.000
rrl1474362r.705a>g1.000
rrl1474374r.717t>g1.000
rrl1474387r.730c>t1.000
rrl1474452r.795c>g1.000
rrl1474552r.895c>t1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t1.000
rrl1474638r.981c>a1.000
rrl1474639r.982g>c1.000
rrl1474710r.1053t>g1.000
rrl1474711r.1054g>t0.588
rrl1474713r.1056t>a0.588
rrl1474715r.1058t>tc1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g0.846
rrl1474777r.1120t>c0.148
rrl1474779r.1122g>a0.154
rrl1474780r.1123c>t0.154
rrl1474782r.1125g>a0.154
rrl1474790r.1133c>t0.138
rrl1474794r.1137c>t0.852
rrl1474798r.1141c>t0.148
rrl1474804r.1147c>t0.160
rrl1474812r.1155g>a0.826
rrl1474827r.1170c>t0.143
rrl1474830r.1173a>g0.828
rrl1474831r.1174a>c0.172
rrl1474844r.1187g>t0.156
rrl1474866r.1209c>a0.128
rrl1475031r.1374g>t1.000
rrl1475037r.1380t>c1.000
rrl1475061r.1404c>t1.000
rrl1475062r.1405a>g1.000
rrl1475120r.1463g>t1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475375r.1718g>a1.000
rrl1475378r.1721a>t1.000
rrl1475379r.1722g>c1.000
rrl1475380r.1723c>a1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>a1.000
rrl1475430r.1773t>a1.000
rrl1475433r.1776a>c1.000
rrl1475436r.1779c>t1.000
rrl1475452r.1795c>a1.000
rrl1475460r.1803a>g1.000
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>g0.952
rrl1475762r.2105g>t0.941
rrl1475763r.2106c>t0.941
rrl1475764r.2107a>c0.941
rrl1475765r.2108a>g0.941
rrl1475775r.2118g>t0.957
rrl1475916r.2259c>t1.000
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475995r.2338g>a1.000
rrl1475997r.2340a>g1.000
rrl1476033r.2376t>c1.000
rrl1476034r.2377c>g1.000
rrl1476035r.2378g>c1.000
rrl1476044r.2387t>g1.000
rrl1476045r.2388g>t1.000
rrl1476049r.2392c>t1.000
rrl1476086r.2429g>a1.000
rrl1476088r.2431a>c0.964
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>g1.000
rrl1476245r.2588c>t1.000
rrl1476246r.2589g>a1.000
rrl1476252r.2595t>g1.000
rrl1476256r.2599a>c1.000
rrl1476262r.2605g>a1.000
rrl1476281r.2624t>c1.000
rrl1476466r.2809c>t0.176
rrl1476529r.2872a>t1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>g1.000
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c1.000
rrl1476665r.3008t>a1.000
rrl1476674r.3017t>c1.000
rrl1476679r.3022t>a1.000
rrl1476689r.3032a>t0.467
rrl1476690r.3033c>t0.500
rrl1476692r.3035t>a1.000
rrl1476693r.3036g>a0.500
rrl1476695r.3038t>a0.462
rrl1476716r.3059a>c1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833970c.429G>T1.000
rpsA1833979c.438T>C1.000
rpsA1834015c.474G>C0.923
rpsA1834042c.501G>A1.000
rpsA1834051c.510G>A1.000
rpsA1834096c.555G>T1.000
rpsA1834097c.556T>A1.000
rpsA1834348c.807T>C1.000
rpsA1834364c.823T>A1.000
rpsA1834375c.834G>T1.000
rpsA1834411c.870T>C1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C1.000
fbiA3640319c.-224A>T1.000
fbiA3640347c.-196A>G1.000
fbiA3640350c.-193C>T1.000
fbiA3640355c.-188C>T1.000
fbiA3640365c.-178C>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;