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: 5d807efc5e335
Sample: 5d807efc5e335

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Summary
ID: 5d807efc5e335
Date: Tue Sep 17 07:57:22 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
RifampicinRrpoB p.His445Asn (0.98)
Ethambutol
Pyrazinamide
StreptomycinRrpsL p.Lys43Arg (0.96), rrs r.517c>t (0.88)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6745c.1506T>C0.143
gyrA7362p.Glu21Gln1.000
gyrA7421c.120G>C0.121
gyrA7585p.Ser95Thr1.000
gyrA7970c.669T>C0.129
gyrA7988c.687G>C0.122
gyrA8294c.993T>C0.195
gyrA9304p.Gly668Asp1.000
rpoB761717c.1911C>G0.164
rpoB762710c.2904G>C0.134
rpoB762736p.Ala977Glu0.134
rpoB762753c.2947T>C0.157
rpoB762758c.2952G>C0.186
rpoB762782c.2976T>C0.289
rpoB762789p.Leu995Met0.304
rpoB762795p.Asp997Asn0.311
rpoB762799p.Ala998Gly0.301
rpoB762813p.Met1003Val0.269
rpoB762818c.3012C>G0.273
rpoB763031c.3225T>C1.000
rpoC763430c.61A>C0.163
rpoC763435c.66A>G0.159
rpoC763666c.297G>C0.145
rpoC763669c.300C>G0.146
rpoC763735c.366G>C0.167
rpoC763765c.396T>C0.186
rpoC763768c.399C>G0.181
rpoC763781p.Ser138Ala0.197
rpoC763792p.Glu141Asp0.180
rpoC764113c.744C>T0.140
rpoC765289c.1920G>C0.274
rpoC765292c.1923G>T0.272
rpoC765305p.Ile646Leu0.258
rpoC765319c.1950A>G0.313
rpoC765326p.His653Ala0.305
rpoC765330p.Ser654Asn0.289
rpoC765349c.1980T>C0.250
rpoC765352c.1983G>C0.257
rpoC765356p.Met663Val0.263
rpoC765370c.2001G>C0.224
rpoC765383p.Met672Leu0.243
rpoC765394c.2025G>A0.205
rpoC765421c.2052C>G0.139
rpoC765946c.2577C>T0.218
rpoC765961c.2592G>A0.179
rpoC765962c.2593T>C0.181
rpoC765967c.2598C>G0.169
rpoC765994c.2625A>T0.176
rpoC766009c.2640G>C0.154
rpoC766010p.Ser881Thr0.154
rpsL781395c.-165T>C0.995
rrl1474957r.1300c>t0.297
rrl1474965r.1308g>a0.273
rrl1474968r.1311g>a0.282
rrl1475006r.1349a>g0.263
rrl1475007r.1350c>t0.241
rrl1475013r.1356g>a0.239
rrl1475018r.1361g>t0.242
rrl1475019r.1362t>a0.239
rrl1475505r.1848g>a0.151
rrl1476214r.2557g>t0.188
rrl1476215r.2558c>t0.191
rrl1476297r.2640c>t0.220
rrl1476299r.2642c>t0.218
inhA1674556p.Gly119Cys0.152
rpsA1834177c.636A>C1.000
rpsA1834396c.855G>C0.174
rpsA1834411c.870T>C0.170
tlyA1917972c.33A>G1.000
katG2153970p.Asp714Glu0.156
katG2154724p.Arg463Leu1.000
kasA2519287c.1173T>C0.162
kasA2519293p.Asp393Glu0.164
kasA2519305c.1191A>G0.158
kasA2519306p.Val398Ile0.158
kasA2519338c.1224T>C0.261
kasA2519341c.1227G>A0.167
kasA2519347c.1233T>C0.178
kasA2519350c.1236C>G0.159
thyX3067849p.Pro33Ser0.134
thyX3067850c.96T>G0.134
thyX3067853c.93G>C0.134
thyX3067862c.84G>A0.131
thyX3067869p.Thr26Ser0.134
ald3086788c.-32T>C1.000
ald3087272c.453A>G0.165
ald3087278c.459A>G0.183
ald3087290c.471T>C0.166
ald3087292p.Val158Ala0.165
alr3841662c.-242A>G0.228
panD4044096c.186G>A0.139
panD4044119c.163G>A0.157
panD4044120c.162T>C0.155
panD4044123c.159A>G0.159
panD4044126c.156A>G0.161
panD4044138c.144A>G0.196
panD4044150c.132T>G0.176
panD4044162c.120T>C0.170
panD4044174c.108G>C0.175
panD4044188c.94A>G0.164
panD4044189c.93G>A0.165
panD4044195c.87A>G0.185
panD4044210c.72G>T0.231
embC4240432c.570C>A0.281
embC4240447c.585G>C0.273
embC4240480c.618G>A0.214
embC4240484p.Ala208Thr0.214
embC4240489c.627A>G0.202
embC4240852c.990G>A0.142
embC4240859p.Leu333Met0.142
embC4240867c.1005T>G0.174
embC4240870c.1008T>C0.164
embC4240875p.Ser338Thr0.190
embC4240886p.Ile342Val0.179
embC4240897c.1035C>G0.133
embC4241161c.1299C>A0.143
embC4241167c.1305C>G0.187
embC4241168c.1306C>T0.183
embC4241206c.1344G>C0.175
embC4241207c.1345C>T0.180
embC4242183p.Ala774Gly0.160
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
embA4245830c.2598G>C0.161
embA4245845c.2613T>C0.188
embA4245848c.2616C>G0.190
embA4245851c.2619G>C0.175
embA4245887c.2655T>C0.133
embB4246544p.Thr11Pro0.181
embB4246548p.Pro12Gln0.650
embB4246555c.42G>C0.640
embB4246556p.Ala15Pro0.642
embB4246563p.Leu17Trp0.319
embB4247998c.1485C>T0.222
embB4248001c.1488C>T0.205
embB4248008c.1495C>T0.214
embB4248013c.1500A>G0.207
embB4248020c.1507T>C0.187
embB4248032c.1519A>C0.189
embB4248037c.1524T>C0.209
embB4248040c.1527C>T0.192
embB4248041p.Ala510Ser0.192
embB4248046c.1533A>G0.201
embB4248055c.1542G>C0.279
embB4248070c.1557T>C0.294
embB4248085c.1572T>C0.294
embB4248097c.1584C>G0.309
embB4248098p.Ile529Phe0.309
embB4248109c.1596C>T0.355
embB4248130c.1617G>C0.248
embB4248133c.1620C>G0.231
embB4248139c.1626C>G0.209
embB4248142c.1629T>C0.208
embB4248149p.Thr546Ala0.243
embB4248157c.1644A>G0.239
embB4248185c.1672T>C0.174
embB4248190c.1677G>C0.179
embB4248283c.1770C>G0.149
embB4248305c.1792C>T0.220
embB4248316c.1803C>G0.253
embB4248319c.1806A>G0.250
embB4248322c.1809G>T0.244
embB4248334c.1821C>G0.232
embB4248338c.1825C>T0.212
embB4248350c.1837T>C0.190
embB4248355c.1842A>G0.194
embB4248358c.1845C>G0.184
embB4248361c.1848A>G0.171
embB4248731p.Val740Leu0.140
embB4248742c.2229T>C0.140
embB4248744p.Val744Ala0.148
embB4248748c.2235C>T0.154
embB4248754c.2241C>T0.192
embB4248772c.2259A>C0.211
embB4249594c.3081G>C0.146
embB4249600c.3087A>G0.149
embB4249627c.3114G>C0.209
embB4249648c.3135G>C0.277
embB4249663c.3150C>G0.188
ethA4326332p.Ala381Val0.147
ethA4326340c.1134G>C0.154
ethA4326351p.Ser375Thr0.154
ethA4326371p.Ala368Val0.857
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;