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: 5d7703f503814
Sample: 5d7703f503814

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Summary
ID: 5d7703f503814
Date: Tue Sep 10 03:02:15 2019
Strain: lineage2.1
Drug-resistance: XDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (0.88)
EthambutolRembB p.Met306Ile (0.84), embB p.His312Arg (0.19)
PyrazinamideRpncA p.Ile90Ser (1.00)
Streptomycin
Ethionamide
FluoroquinolonesRgyrA p.Asp94Gly (0.81)
AmikacinRrrs r.1401a>g (0.92)
CapreomycinRrrs r.1401a>g (0.92)
KanamycinRrrs r.1401a>g (0.92)

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5341c.102T>C0.135
gyrB5383c.144G>A0.871
gyrA7362p.Glu21Gln1.000
gyrA7541c.240C>G0.161
gyrA7559c.258G>A0.172
gyrA7585p.Ser95Thr1.000
gyrA8375c.1074G>C0.158
gyrA8382p.Leu361Met0.176
gyrA8393c.1092T>C0.167
gyrA8399c.1098T>C0.161
gyrA8402p.Asp367Glu0.152
gyrA8546c.1245T>C0.148
gyrA8585c.1284C>T0.211
gyrA8603c.1302A>C0.222
gyrA8624c.1323G>T0.190
gyrA8633c.1332C>G0.190
gyrA8645c.1344C>T0.211
gyrA8655p.Ile452Val0.278
gyrA8666c.1365G>C0.278
gyrA8672c.1371A>G0.294
gyrA8693c.1392T>C0.308
gyrA8711c.1410A>C0.273
gyrA8714c.1413A>G0.273
gyrA8723c.1422G>A0.273
gyrA8729c.1428T>C0.273
gyrA8732c.1431G>C0.250
gyrA8897c.1596T>C0.200
gyrA8903c.1602T>C0.176
gyrA8912c.1611G>A0.194
gyrA8915c.1614A>G0.188
gyrA8924c.1623C>G0.188
gyrA8933c.1632G>A0.182
gyrA8939c.1638T>C0.171
gyrA8942c.1641G>C0.171
gyrA8945c.1644G>T0.167
gyrA8946c.1645T>C0.167
gyrA8981c.1680G>C0.175
gyrA8987c.1686C>G0.194
gyrA8996c.1695T>C0.179
gyrA8998p.Leu566Trp0.158
gyrA9003c.1702C>T0.158
gyrA9017c.1716C>T0.184
gyrA9023c.1722A>C0.179
gyrA9029c.1728T>G0.152
gyrA9032c.1731T>C0.176
gyrA9035c.1734G>T0.161
gyrA9050p.Asp583Glu0.188
gyrA9068c.1767G>C0.267
gyrA9071c.1770G>C0.217
gyrA9080c.1779G>C0.217
gyrA9089c.1788G>C0.217
gyrA9101c.1800A>G0.192
gyrA9119c.1818A>G0.185
gyrA9143c.1842T>C0.185
gyrA9304p.Gly668Asp1.000
rpoB760184c.378A>G0.128
rpoB760235c.429T>C0.171
rpoB760256c.450C>T0.135
rpoB760328c.522G>C0.136
rpoB760343c.537G>C0.136
rpoB760564p.Arg253Leu0.138
rpoB761168c.1362C>G0.129
rpoB761180c.1374A>C0.125
rpoB761195c.1389G>C0.129
rpoB761201c.1395G>A0.129
rpoB761219c.1413G>T0.184
rpoB761249c.1443A>G0.200
rpoB761255c.1449T>G0.171
rpoB761261c.1455G>T0.182
rpoB761273c.1467T>C0.143
rpoB761282c.1476C>A0.152
rpoB761537c.1731C>A0.182
rpoB761543c.1737G>A0.174
rpoB761570c.1764T>C0.174
rpoB761573c.1767C>G0.143
rpoB762209c.2403C>G0.150
rpoB762995c.3189G>T0.146
rpoB763028c.3222T>C0.206
rpoB763031c.3225T>C0.212
rpoB763034c.3228C>G0.206
rpoB763040c.3234C>G0.200
rpoB763043c.3237G>A0.200
rpoB763070c.3264T>C0.321
rpoB763085c.3279C>G0.310
rpoB763094c.3288G>C0.241
rpoB763115c.3309T>C0.207
rpoB763145c.3339G>A0.222
rpoB763166c.3360A>G0.192
rpoC763375c.6C>A0.122
rpoC763408c.39T>C0.132
rpoC763411c.42T>G0.132
rpoC763414c.45T>C0.132
rpoC763430c.61A>C0.140
rpoC763444c.75T>C0.122
rpoC763456c.87A>G0.150
rpoC763486c.117T>C0.167
rpoC763492c.123G>C0.138
rpoC764185c.816C>A0.211
rpoC764188c.819A>G0.211
rpoC764195p.Ser276Ala0.222
rpoC764203c.834G>C0.222
rpoC764206p.Asp279Glu0.235
rpoC764217p.Asn283Ser0.235
rpoC764236c.867G>A0.211
rpoC764245c.876C>T0.211
rpoC764266c.897T>C0.267
rpoC764269c.900G>C0.267
rpoC764278c.909A>G0.267
rpoC764497c.1128A>G0.152
rpoC764500c.1131C>G0.167
rpoC764521c.1152T>C0.167
rpoC764524c.1155C>A0.167
rpoC764527c.1158C>T0.179
rpoC764539c.1170C>T0.179
rpoC764542c.1173C>T0.179
rpoC764554c.1185C>T0.250
rpoC764566c.1197C>G0.227
rpoC764653c.1284G>C0.167
rpoC764656c.1287C>T0.182
rpoC764668c.1299C>T0.174
rpoC764686c.1317C>T0.214
rpoC764734c.1365C>T0.235
rpoC764749c.1380G>C0.216
rpoC764752c.1383G>C0.211
rpoC764764c.1395T>C0.200
rpoC764791c.1422C>G0.146
rpoC764800c.1431G>A0.132
rpoC764803c.1434C>T0.125
rpoC764809c.1440C>T0.143
rpoC764812c.1443C>G0.143
rpoC764815c.1446A>G0.152
rpoC764830c.1461C>G0.122
rpoC764833c.1464A>G0.122
rpoC764931p.Ala521Asp0.902
rpoC765121c.1752G>A1.000
rpoC765529c.2160C>G0.179
rpoC765541c.2172C>G0.185
rpoC765547c.2178C>A0.167
rpoC765556c.2187G>C0.179
rpoC765562c.2193G>C0.179
rpoC765580c.2211G>C0.160
rpoC765583c.2214G>T0.160
rpoC765628c.2259G>C0.161
rpoC765883c.2514C>G0.160
rpoC765886c.2517C>G0.154
rpsL781395c.-165T>C1.000
rpsL781571c.12C>T0.167
rpsL781586c.27C>A0.182
rpsL781608p.Ser17Ala0.171
rpsL781631c.72G>C0.167
rpsL781649c.90T>C0.152
rpsL781655c.96T>C0.143
rpsL781658c.99A>G0.135
rpsL781808c.249C>T0.150
rpsL781847c.288G>A0.208
rpsL781865c.306G>C0.250
rpsL781868c.309T>C0.250
rpsL781871c.312G>C0.238
rpsL781877c.318T>A0.250
rpsL781880c.321C>G0.238
rpsL781892c.333A>G0.250
rpsL781898c.339A>T0.250
rpsL781916c.357T>C0.273
rpsL781929p.Gly124Ser0.304
rplC800844c.36T>C0.128
rplC800865c.57A>G0.156
rplC800867p.Ser20Asn0.152
rplC800877c.69A>C0.139
rplC800889c.81C>A0.129
rplC800901c.93C>A0.147
rplC800907c.99C>G0.182
rplC800913c.105G>C0.171
rplC800916c.108A>G0.176
rplC800919c.111C>G0.194
rplC800934c.126C>G0.200
rplC800937c.129A>G0.176
rplC801027c.219C>A0.150
rrs1471969r.124t>c0.167
rrs1471970r.125g>a0.159
rrs1471984r.139t>a0.143
rrs1471985r.140t>c0.143
rrs1472061r.216a>t0.121
rrs1472075r.230a>g0.132
rrl1473877r.220g>a0.151
rrl1473887r.230t>a0.137
rrl1473888r.231t>a0.157
rrl1473898r.241c>t0.149
rrl1473899r.242a>c0.149
rrl1474083r.426c>t0.189
rrl1474103r.446a>t0.179
rrl1474140r.483c>t0.167
rrl1474151r.494c>t0.179
rrl1474181r.524c>t0.196
rrl1474201r.544t>a0.254
rrl1474362r.705a>g0.143
rrl1474374r.717t>a0.130
rrl1474376r.719t>c0.130
rrl1474794r.1137c>a0.152
rrl1475006r.1349a>g0.156
rrl1475061r.1404c>t0.211
rrl1475429r.1772g>a0.156
rrl1475526r.1869c>a0.146
rrl1475988r.2331a>g0.189
rrl1476035r.2378g>a0.216
rrl1476529r.2872a>g0.184
rrl1476580r.2923g>a0.205
rrl1476597r.2940g>a0.195
rrl1476619r.2962c>t0.163
rrl1476628r.2971t>a0.156
rrl1476679r.3022t>c0.143
fabG11674018c.579G>A0.152
fabG11674033c.594T>C0.152
fabG11674037p.Gln200Glu0.152
fabG11674045c.606G>A0.188
fabG11674054c.615T>C0.188
fabG11674060c.621A>G0.200
fabG11674075c.636C>A0.172
fabG11674078c.639C>G0.167
fabG11674079p.Pro214Ala0.167
inhA1674870c.669T>C0.150
rpsA1833847c.306C>G0.129
rpsA1833856c.315A>G0.138
rpsA1833862c.321G>A0.154
rpsA1833979c.438T>C0.200
rpsA1834000c.459G>C0.208
rpsA1834015c.474G>T0.333
rpsA1834024c.483G>A0.400
rpsA1834030c.489C>G0.370
rpsA1834051c.510G>A0.417
rpsA1834093c.552G>C0.360
rpsA1834102c.561T>G0.391
rpsA1834105c.564C>G0.375
rpsA1834123c.582C>G0.276
rpsA1834177c.636A>C1.000
rpsA1834261c.720A>C0.150
rpsA1834264c.723G>C0.150
rpsA1834639c.1098T>C0.143
rpsA1834684c.1143C>A0.222
rpsA1834690c.1149T>C0.205
rpsA1834733p.Ala398Pro0.150
rpsA1834738p.Glu399Asp0.143
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518312c.198T>C0.143
kasA2518323p.Ser70Asn0.167
kasA2518408c.294C>G0.150
kasA2518778p.Glu222Gln0.235
kasA2518783c.669T>C0.222
kasA2518789c.675G>T0.211
kasA2518795c.681C>G0.148
kasA2518816c.702C>G0.138
kasA2518825c.711T>C0.129
kasA2518855c.741C>G0.143
kasA2518856p.Ile248Leu0.147
kasA2518864c.750G>C0.143
kasA2518879c.765A>G0.135
kasA2518882c.768C>T0.139
kasA2518885c.771T>C0.143
kasA2519059c.945G>A0.238
kasA2519062c.948T>G0.286
kasA2519074c.960C>G0.250
kasA2519077c.963G>C0.267
kasA2519095c.981C>G0.250
kasA2519110p.Asp332Glu0.250
folC2747089c.510C>G0.143
folC2747101c.498C>T0.143
folC2747110c.489A>G0.136
thyX3067814c.132A>G0.176
thyX3067820c.126G>C0.200
thyX3067832c.114G>A0.214
thyX3067838c.108G>C0.222
thyX3067843c.103G>A0.214
thyX3067849p.Pro33Ser0.214
thyX3067850c.96T>G0.214
thyX3067874c.72G>C0.167
thyX3067885p.Pro21Ser0.190
thyX3067886c.60T>C0.190
thyX3067889c.57G>C0.182
thyX3067893p.Leu18Trp0.174
thyX3067898p.Asp16Glu0.190
thyX3067916p.Gln10His0.174
thyA3074252p.Glu74Gln0.133
thyA3074262c.210A>G0.143
thyA3074274c.198A>G0.138
thyA3074277c.195G>C0.138
thyA3074297c.175G>A0.143
thyA3074307c.165T>G0.138
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.194
alr3841654c.-234A>C0.205
embA4244822c.1590G>A0.238
embA4244823p.Val531Met0.238
embA4244843c.1611G>C0.263
embA4244856p.Ala542Pro0.238
embA4244873c.1641C>T0.227
embA4244885c.1653A>G0.250
embA4244888c.1656G>C0.250
embA4244894c.1662C>T0.263
embA4244897c.1665T>G0.263
embA4244904p.Val558Ile0.250
embA4244919c.1687C>T0.200
embA4244930c.1698G>C0.190
embA4244933c.1701A>C0.182
embA4245101c.1869G>C0.167
embA4245125c.1893G>A0.190
embA4245137c.1905T>C0.211
embA4245173c.1941G>C0.250
embA4245182c.1950T>C0.231
embA4245188c.1956G>C0.250
embA4245206c.1974A>T0.182
embA4245207c.1975T>C0.182
embA4245215c.1983A>C0.182
embA4245224c.1992T>C0.167
embA4245662c.2430G>C0.188
embA4245671c.2439C>G0.200
embA4245674c.2442A>C0.200
embA4245677c.2445G>C0.188
embA4245686c.2454G>C0.214
embA4245692c.2460G>A0.200
embA4245693p.Ile821Val0.188
embA4245764c.2532G>C0.188
embA4245772p.Asn847Thr0.176
embA4246041p.Asp937Thr0.158
embA4246064c.2832T>C0.158
embA4246088c.2856A>G1.000
embB4247437c.924A>C0.176
embB4247458c.945C>T0.176
embB4247470c.957T>C0.176
embB4247473c.960C>T0.176
embB4247491c.978G>C0.176
embB4247497c.984T>C0.176
embB4247500c.987C>G0.176
embB4247512c.999T>C0.167
embB4248052c.1539G>T0.171
embB4248055c.1542G>C0.194
embB4248064c.1551G>C0.189
embB4248070c.1557T>C0.184
embB4248076c.1563G>A0.212
embB4248085c.1572T>C0.206
embB4248118c.1605T>C0.241
embB4248130c.1617G>C0.286
embB4248154c.1641G>C0.290
embB4248157c.1644A>G0.290
embB4248163c.1650G>A0.300
embB4248178c.1665C>T0.179
embB4248206p.Ser565Gly0.136
embB4248277c.1764G>C0.154
embB4248328c.1815G>A0.143
embB4248355c.1842A>G0.148
embB4248358c.1845C>A0.148
embB4248362p.Ser617Gln0.143
ethA4326919c.555T>G0.143
ethA4326928c.546G>T0.148
ethA4326950p.Ala175Gly0.160
ethA4326952p.Asp174Glu0.167
gid4407588c.615T>C1.000
gid4407985p.Gly73Ala1.000

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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