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: 5db3b34c423fa
Sample: 5db3b34c423fa

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Summary
ID: 5db3b34c423fa
Date: Sat Oct 26 03:53:33 2019
Strain: lineage3;lineage4.3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (0.23)
Pyrazinamide
StreptomycinRrrs r.462c>t (0.21)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage3East-African-IndianCASRD750
lineage4.3Euro-American (LAM)mainly-LAMNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6196c.957C>T0.191
gyrB6215p.Ser326Thr0.131
gyrB6760c.1521G>C0.149
gyrB6775c.1536G>C0.158
gyrB6787c.1548G>A0.147
gyrB6793c.1554T>C0.135
gyrB6797p.Gly520Thr0.133
gyrB7147c.1908G>C0.141
gyrB7165c.1926C>G0.196
gyrB7178c.1939T>C0.252
gyrB7216c.1977G>C0.212
gyrB7237c.1998C>T0.135
gyrA7362p.Glu21Gln1.000
gyrA7391c.90C>T0.256
gyrA7394c.93T>C0.274
gyrA7427c.126G>C0.261
gyrA7442c.141G>T0.168
gyrA7451c.150C>G0.137
gyrA7585p.Ser95Thr1.000
gyrA7793c.492G>C0.135
gyrA7799c.498A>G0.178
gyrA7832c.531G>T0.222
gyrA7835c.534A>C0.219
gyrA7859c.558A>G0.200
gyrA7865c.564T>C0.178
gyrA7868c.567C>T0.175
gyrA8135c.834C>G0.142
gyrA8156c.855T>C0.167
gyrA8168c.867A>G0.169
gyrA8177c.876A>C0.171
gyrA8198c.897T>C0.170
gyrA8546p.Asp415Glu0.158
gyrA8552c.1251C>G0.184
gyrA8561c.1260A>C0.218
gyrA8576c.1275C>G0.221
gyrA8603c.1302A>G0.220
gyrA8619c.1318T>C0.153
gyrA8624c.1323G>C0.137
gyrA9296c.1995T>C0.205
gyrA9299c.1998G>C0.205
gyrA9304p.Gly668Glu1.000
gyrA9335c.2034G>C0.343
gyrA9345c.2044A>C0.348
gyrA9365c.2064G>A0.266
gyrA9377c.2076A>G0.216
gyrA9383c.2082T>C0.187
rpoB759606c.-201T>C0.288
rpoB759629c.-178T>C0.198
rpoB759644c.-163T>A0.140
rpoB759647c.-160T>C0.128
rpoB760067c.261G>C0.125
rpoB760070c.264T>G0.120
rpoB760091c.285G>C0.125
rpoB760101c.295T>C0.143
rpoB760112c.306T>C0.164
rpoB760118c.312T>C0.155
rpoB760130p.Asp108Glu0.148
rpoB760139c.333A>G0.174
rpoB760142c.336C>G0.172
rpoB760181c.375T>C0.250
rpoB760184c.378A>G0.252
rpoB760196c.390C>G0.283
rpoB760223c.417T>C0.235
rpoB760235c.429T>C0.242
rpoB760244c.438G>C0.267
rpoB760256c.450C>T0.278
rpoB760274c.468G>A0.223
rpoB760283c.477G>C0.204
rpoB760328c.522G>C0.176
rpoB760331c.525G>C0.165
rpoB760337c.531C>G0.153
rpoB760340c.534G>C0.146
rpoB760361c.555T>C0.185
rpoB760370c.564C>G0.170
rpoB760376p.Asp190Glu0.153
rpoB760380p.Thr192Leu0.141
rpoB760424c.618C>G0.200
rpoB760430c.624T>C0.177
rpoB760460c.654G>C0.148
rpoB760591p.Val262Ala0.221
rpoB760598c.792C>T0.228
rpoB760611c.805T>C0.221
rpoB760646c.840C>G0.149
rpoB760655c.849A>G0.153
rpoB760724c.918T>C0.152
rpoB760730c.924T>C0.154
rpoB760886c.1080A>G0.125
rpoB760919c.1113C>G0.274
rpoB760925c.1119T>C0.273
rpoB760928c.1122G>C0.270
rpoB760931c.1125C>G0.286
rpoB760946c.1140A>G0.320
rpoB760982c.1176G>C0.200
rpoB760991c.1185G>T0.182
rpoB761006c.1200C>G0.141
rpoB761015c.1209G>C0.143
rpoB761027c.1221A>G0.163
rpoB761036c.1230G>C0.128
rpoB761037c.1231T>C0.139
rpoB761057c.1251G>C0.253
rpoB761097c.1291A>T0.160
rpoB761102c.1296A>G0.162
rpoB761180c.1374A>C0.189
rpoB761189c.1383T>C0.194
rpoB761195c.1389G>C0.220
rpoB761207c.1401C>T0.242
rpoB761234c.1428G>C0.267
rpoB761249c.1443A>G0.230
rpoB761255c.1449T>G0.227
rpoB761261c.1455G>T0.211
rpoB761264c.1458C>G0.190
rpoB761300c.1494G>C0.261
rpoB761318c.1512G>C0.220
rpoB761327c.1521A>G0.181
rpoB761345c.1539G>C0.132
rpoB761492c.1686G>C0.145
rpoB761504c.1698C>G0.143
rpoB761510c.1704T>C0.133
rpoB761537c.1731C>G0.117
rpoB761969c.2163G>A0.142
rpoB761972c.2166C>G0.161
rpoB761999c.2193G>C0.230
rpoB762008c.2202C>G0.250
rpoB762014c.2208C>T0.250
rpoB762017c.2211A>G0.236
rpoB762053c.2247T>C0.210
rpoB762062c.2256T>C0.177
rpoB762065c.2259T>C0.171
rpoB762083c.2277T>C0.133
rpoB762101c.2295C>G0.124
rpoB762114p.Ile770Val0.128
rpoB762131c.2325C>G0.177
rpoB762143c.2337T>C0.203
rpoB762149c.2343G>C0.195
rpoB762176c.2370T>C0.233
rpoB762185c.2379G>C0.247
rpoB762233c.2427G>C0.261
rpoB762254c.2448T>C0.279
rpoB762257c.2451C>G0.276
rpoB762284c.2478G>T0.264
rpoB762293c.2487T>C0.237
rpoB762296c.2490G>C0.197
rpoB762317c.2511A>G0.163
rpoB762434c.2628T>G0.897
rpoB762857c.3051C>G0.134
rpoB762860c.3054G>C0.143
rpoB762863c.3057T>G0.151
rpoB762899c.3093G>C0.322
rpoB762929c.3123G>T0.359
rpoB762947c.3141C>G0.310
rpoB762962c.3156C>T0.305
rpoB762983c.3177C>T0.231
rpoB762989c.3183G>C0.230
rpoB762995c.3189G>T0.239
rpoB763028c.3222T>C0.211
rpoB763031c.3225T>C0.211
rpoB763034c.3228C>G0.205
rpoB763040c.3234C>G0.238
rpoB763070c.3264T>C0.275
rpoB763085c.3279C>G0.282
rpoB763115c.3309T>C0.288
rpoB763139c.3333C>T0.294
rpoB763148c.3342G>C0.267
rpoB763158c.3352C>T0.211
rpoB763166c.3360A>G0.172
rpoC763351c.-19T>C0.135
rpoC763352c.-18T>A0.156
rpoC763402c.33C>T0.268
rpoC763408c.39T>C0.224
rpoC763411c.42T>G0.217
rpoC763414c.45T>C0.211
rpoC763441c.72C>T0.149
rpoC763444c.75T>C0.142
rpoC763456c.87A>G0.151
rpoC763486c.117T>G0.250
rpoC763528c.159G>A0.360
rpoC763546c.177A>G0.321
rpoC763570c.201G>C0.247
rpoC763573c.204G>C0.258
rpoC763576c.207C>G0.245
rpoC763594c.225C>T0.252
rpoC763603c.234C>T0.218
rpoC763636c.267T>C0.276
rpoC763660c.291T>G0.233
rpoC763663c.294C>G0.228
rpoC763675c.306C>G0.202
rpoC763930c.561G>A0.312
rpoC763945c.576T>C0.278
rpoC763951c.582G>C0.274
rpoC763960c.591T>C0.234
rpoC764112p.Tyr248Phe0.152
rpoC764116c.747C>T0.168
rpoC764131c.762T>C0.202
rpoC764134c.765C>G0.216
rpoC764198c.829C>T0.232
rpoC764203c.834G>T0.226
rpoC764206c.837T>C0.226
rpoC764213p.Arg282Lys0.213
rpoC764257c.888G>C0.347
rpoC764266c.897T>C0.356
rpoC764269c.900G>C0.366
rpoC764278c.909A>G0.414
rpoC764287c.918C>T0.421
rpoC764293c.924G>C0.430
rpoC764338c.969G>A0.461
rpoC764365c.996C>T0.324
rpoC764380c.1011G>C0.154
rpoC764383c.1014C>G0.111
rpoC764497c.1128A>G0.161
rpoC764500c.1131C>G0.167
rpoC764521c.1152T>C0.185
rpoC764527c.1158C>T0.173
rpoC764536c.1167G>C0.164
rpoC764539c.1170C>G0.159
rpoC764593c.1224C>T0.122
rpoC764611c.1242G>C0.208
rpoC764626c.1257C>T0.262
rpoC764650c.1281G>T0.308
rpoC764668c.1299C>T0.351
rpoC764764c.1395T>C0.315
rpoC764803c.1434C>T0.344
rpoC764809c.1440C>T0.337
rpoC764815c.1446A>G0.341
rpoC764827c.1458G>C0.320
rpoC764858c.1489T>C0.361
rpoC764872c.1503A>G0.415
rpoC764888c.1519T>C0.358
rpoC764932c.1563C>G0.292
rpoC764935c.1566T>C0.287
rpoC764948c.1579T>C0.255
rpoC764968c.1599T>C0.210
rpoC764995c.1626C>G0.170
rpoC765300p.Val644Ala0.134
rpoC765319c.1950A>G0.129
rpoC765421c.2052C>G0.137
rpoC765451c.2082C>G0.230
rpoC765454c.2085C>G0.262
rpoC765469c.2100G>C0.292
rpoC765478c.2109T>C0.306
rpoC765499c.2130C>G0.282
rpoC765508c.2139C>G0.259
rpoC765529c.2160C>T0.163
rpoC765613p.His748Gln0.203
rpoC765625c.2256C>G0.238
rpoC765628c.2259G>C0.233
rpoC765631p.Asp754Glu0.238
rpoC765658c.2289C>T0.304
rpoC765700c.2331T>C0.304
rpoC765734c.2365T>C0.220
rpoC765739c.2370G>T0.193
rpoC765751c.2382C>G0.130
rpoC765753p.Asp795Ala0.125
rpoC765811c.2442T>G0.184
rpoC765826c.2457T>C0.259
rpoC765886c.2517C>G0.333
rpoC765928c.2559C>G0.279
rpoC765967c.2598C>T0.148
rpoC766408c.3039C>T0.200
rpoC766411c.3042C>G0.207
rpoC766426c.3057C>T0.248
rpoC766447c.3078T>C0.259
rpoC766462c.3093G>T0.224
rpoC766522c.3153C>G0.143
rpoC766531c.3162G>T0.148
rpoC766543c.3174C>T0.172
rpoC766630c.3261G>T0.168
rpoC766645c.3276A>G0.255
rpoC766657c.3288A>G0.275
rpoC766666c.3297C>G0.281
rpoC766672c.3303T>C0.322
rpoC766726c.3357T>C0.361
rpoC766738c.3369G>C0.370
rpoC766765c.3396A>C0.358
rpoC766774c.3405T>C0.368
rpoC766804c.3435A>G0.395
rpoC766861c.3492G>C0.262
rpoC766864c.3495G>C0.244
rpoC766867c.3498C>G0.237
rpoC767032c.3663G>A0.207
rpoC767059c.3690T>G0.200
rpoC767062c.3693C>A0.210
rpoC767098c.3729T>C0.202
rpoC767104c.3735C>G0.122
rpoC767119c.3750A>G0.173
rpoC767134c.3765C>A0.202
rpoC767167c.3798C>G0.124
rpsL781395c.-165T>C1.000
rpsL781628c.69T>C0.141
rpsL781634c.75G>A0.176
rpsL781649c.90T>C0.202
rpsL781655c.96T>C0.214
rpsL781682c.123T>C0.237
rpsL781728c.169T>C0.126
rpsL781742c.183C>T0.146
rpsL781751c.192G>C0.173
rpsL781754c.195G>C0.207
rpsL781814c.255C>T0.322
rpsL781817c.258G>T0.322
rpsL781832c.273T>C0.241
rpsL781838c.279G>C0.188
rpsL781841c.282C>G0.182
rpsL781929p.Gly124Ser0.164
rrs1471923r.78t>c0.163
rrs1471934r.89a>g0.185
rrs1471969r.124t>c0.180
rrs1471970r.125g>a0.179
rrs1472075r.230a>g0.158
rrs1472108r.263c>t0.227
rrs1472857r.1012a>g0.716
rrs1472969r.1124a>g0.117
rrs1472970r.1125c>g0.115
rrs1472977r.1132g>c0.142
rrs1472978r.1133t>c0.143
rrs1473104r.1259c>t0.282
rrs1473105r.1260g>a0.271
rrs1473123r.1278a>t0.192
rrs1473145r.1300c>t0.235
rrs1473166r.1321g>a0.254
rrs1473288r.1443c>t0.170
rrs1473290r.1445c>t0.160
rrs1473291r.1446g>t0.160
rrl1473668r.11c>t0.153
rrl1473756r.99g>a0.229
rrl1473758r.101g>t0.231
rrl1473806r.149c>t0.260
rrl1473813r.156c>t0.278
rrl1473839r.182g>t0.272
rrl1473877r.220g>a0.217
rrl1473898r.241c>t0.175
rrl1473899r.242a>c0.172
rrl1474036r.379g>a0.143
rrl1474054r.397t>c0.206
rrl1474093r.436g>t0.221
rrl1474099r.442g>a0.233
rrl1474103r.446a>t0.227
rrl1474111r.454t>c0.244
rrl1474140r.483c>t0.282
rrl1474151r.494c>t0.338
rrl1474181r.524c>t0.341
rrl1474249r.592g>t0.178
rrl1474356r.699t>c0.227
rrl1474362r.705a>g0.224
rrl1474376r.719t>c0.213
rrl1474639r.982g>a0.217
rrl1474794r.1137c>t0.269
rrl1474812r.1155g>a0.269
rrl1474823r.1166c>t0.269
rrl1474831r.1174a>g0.324
rrl1474904r.1247g>a0.316
rrl1474956r.1299c>t0.138
rrl1474960r.1303c>g0.138
rrl1474963r.1306g>t0.127
rrl1474964r.1307t>a0.127
rrl1474965r.1308g>c0.143
rrl1474970r.1313g>a0.136
rrl1475006r.1349a>t0.226
rrl1475013r.1356g>a0.203
rrl1475028r.1371g>a0.205
rrl1475061r.1404c>t0.178
rrl1475088r.1431a>t0.159
rrl1475199r.1542g>a0.185
rrl1475201r.1544g>a0.161
rrl1475206r.1549c>t0.164
rrl1475209r.1552g>c0.155
rrl1475213r.1556c>t0.148
rrl1475291r.1634a>c0.210
rrl1475315r.1658a>t0.306
rrl1475355r.1698c>t0.333
rrl1475369r.1712g>t0.299
rrl1475402r.1745c>t0.276
rrl1475409r.1752t>c0.263
rrl1475419r.1762c>t0.268
rrl1475429r.1772g>a0.279
rrl1475483r.1826c>t0.265
rrl1475505r.1848g>a0.306
rrl1475526r.1869c>a0.307
rrl1475599r.1942a>g0.375
rrl1475608r.1951t>c0.344
rrl1475638r.1981c>t0.258
rrl1475642r.1985t>c0.282
rrl1475657r.2000a>g0.256
rrl1475659r.2002g>t0.244
rrl1475763r.2106c>t0.152
rrl1475881r.2224t>c0.378
rrl1475988r.2331a>g0.264
rrl1476115r.2458t>c0.130
rrl1476117r.2460g>c0.127
rrl1476214r.2557g>t0.269
rrl1476215r.2558c>t0.266
rrl1476224r.2567a>g0.297
rrl1476281r.2624t>c0.353
rrl1476297r.2640c>t0.319
rrl1476299r.2642c>t0.326
rrl1476583r.2926g>a0.252
rrl1476584r.2927c>t0.262
rrl1476597r.2940g>a0.261
rrl1476608r.2951c>g0.255
rrl1476628r.2971t>a0.316
fabG11673499c.60T>C0.126
fabG11673505c.66A>C0.129
fabG11673547c.108T>C0.194
inhA1674471c.270G>T0.158
inhA1674480c.279T>C0.148
inhA1674486c.285T>C0.136
inhA1674489c.288G>T0.165
inhA1674537c.336C>G0.154
inhA1674542p.Ala114Glu0.142
inhA1674627c.426T>C0.127
inhA1674636c.435C>G0.158
inhA1674651c.450C>T0.183
inhA1674690c.489C>G0.121
inhA1674870c.669T>C0.133
inhA1674879c.678T>C0.151
rpsA1833554p.Thr5Ala0.221
rpsA1833589c.48A>T0.224
rpsA1833595c.54T>G0.239
rpsA1833667c.126C>G0.286
rpsA1833703c.162C>T0.274
rpsA1833724c.183C>G0.194
rpsA1833727c.186G>C0.187
rpsA1833745c.204G>C0.229
rpsA1833760c.219C>T0.235
rpsA1833793c.252C>T0.236
rpsA1833811c.270G>C0.191
rpsA1833847c.306C>G0.149
rpsA1833856c.315A>G0.177
rpsA1833874c.333T>C0.181
rpsA1833928c.387G>C0.285
rpsA1833971c.430C>T0.250
rpsA1833979c.438T>C0.214
rpsA1834000c.459G>C0.263
rpsA1834021c.480C>T0.270
rpsA1834030c.489C>G0.291
rpsA1834097c.556T>A0.235
rpsA1834102c.561T>G0.230
rpsA1834186c.645C>G0.167
rpsA1834192c.651C>G0.188
rpsA1834222c.681T>C0.250
rpsA1834240c.699T>C0.260
rpsA1834249c.708T>C0.219
rpsA1834261c.720A>G0.216
rpsA1834264c.723G>C0.193
rpsA1834294c.753G>T0.172
rpsA1834297c.756C>T0.173
rpsA1834303c.762T>C0.167
rpsA1834306c.765T>C0.160
rpsA1834348c.807T>C0.220
rpsA1834366c.825A>G0.211
rpsA1834369c.828C>G0.214
rpsA1834396c.855G>C0.185
rpsA1834411c.870T>C0.147
rpsA1834474c.933C>G0.123
rpsA1834477c.936C>T0.129
rpsA1834489c.948T>C0.223
rpsA1834516c.975G>A0.306
rpsA1834528c.987T>C0.321
rpsA1834540c.999G>T0.304
rpsA1834546c.1005T>C0.304
rpsA1834555c.1014T>C0.287
rpsA1834606c.1065C>G0.259
rpsA1834609c.1068T>C0.237
rpsA1834633c.1092A>G0.248
rpsA1834639c.1098T>C0.244
rpsA1834654p.Glu371Asp0.226
rpsA1834669c.1128G>C0.213
rpsA1834690c.1149T>C0.213
rpsA1834732c.1191T>C0.182
rpsA1834738c.1197A>G0.168
rpsA1834789c.1248T>C0.126
rpsA1834792c.1251G>C0.150
rpsA1834828c.1287C>G0.232
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518220c.106C>T0.182
kasA2518234c.120G>A0.184
kasA2518248p.Ala45Val0.163
kasA2518723c.609G>A0.137
kasA2518747c.633C>G0.180
kasA2518768c.654C>G0.184
kasA2518777c.663C>T0.171
ahpC2726105c.-88G>A1.000
folC2747023c.576G>C0.193
folC2747032c.567T>G0.250
folC2747059c.540A>G0.260
folC2747086c.513T>G0.163
folC2747089c.510C>G0.135
folC2747265p.Gly112Ser0.122
folC2747317c.282G>C0.137
folC2747343p.Val86Ile0.140
folC2747355p.Val82Ile0.152
folC2747359c.240G>C0.147
thyX3067349c.597C>G0.213
thyX3067355c.591T>G0.224
thyX3067373c.573G>C0.232
thyX3067394c.552C>G0.239
thyX3067406c.540T>C0.232
thyX3067412c.534G>C0.221
thyX3067427c.519C>G0.171
thyX3067838c.108G>C0.176
thyX3067850c.96T>G0.173
thyX3067869p.Thr26Ser0.213
thyX3067874c.72G>C0.217
thyX3067883c.63G>C0.180
thyX3067886c.60T>G0.174
thyX3067889c.57G>C0.159
thyX3067935p.Thr4Ile0.257
thyA3073959c.513A>G0.238
thyA3073977c.495T>C0.230
thyA3073989c.483A>G0.243
thyA3074001c.471G>C0.175
thyA3074004c.468A>G0.167
thyA3074010c.462G>C0.144
ald3086788c.-32T>C1.000
alr3840636p.Pro262Gln1.000
embC4240685p.Thr275Ala0.148
embC4240693c.831T>C0.205
embC4240698p.Ala279Gly0.221
embC4240726c.864G>C0.301
embC4240780c.918T>C0.250
embC4240783c.921G>C0.267
embC4240789c.927T>C0.282
embC4240807c.945C>T0.325
embC4240819c.957A>G0.311
embC4240831c.969T>G0.253
embC4240859p.Leu333Val0.200
embC4240867c.1005T>C0.141
embC4241107c.1245G>C0.348
embC4241129c.1267C>T0.336
embC4241140c.1278A>G0.339
embC4241158c.1296T>C0.270
embC4241161c.1299C>T0.248
embC4241162c.1300T>C0.244
embC4241203c.1341T>C0.275
embC4241230c.1368A>G0.188
embC4241449c.1587C>G0.217
embC4241452c.1590G>C0.217
embC4241453p.Ile531Val0.222
embC4242075p.Arg738Gln1.000
embC4242643c.2781C>T1.000
embA4245137c.1905T>C0.164
embA4245143c.1911C>T0.161
embA4245149c.1917C>G0.138
embA4245883p.Gly884Asp1.000
embA4246331c.3099C>T0.308
embA4246338p.Leu1036Met0.323
embA4246361c.3129C>G0.338
embA4246383p.Tyr1051His0.307
embA4246400c.3168G>C0.182
embA4246403c.3171G>C0.154
embB4247401c.888T>C0.141
embB4247437c.924A>C0.217
embB4247464c.951C>G0.299
embB4247470c.957T>C0.270
embB4247476c.963C>T0.272
embB4247491c.978G>C0.222
embB4247497c.984T>C0.205
embB4247512c.999T>C0.234
embB4247544p.Ser344Thr0.152
embB4247940p.Leu476Trp0.129
embB4247945c.1432T>C0.130
embB4247951p.Ser480Ala0.148
embB4247974c.1461C>G0.221
embB4247980c.1467C>A0.271
embB4248007c.1494C>G0.238
embB4248035p.Val508Ile0.132
embB4248220c.1707A>G0.234
embB4248226c.1713G>C0.244
embB4248277c.1764G>C0.462
embB4248316c.1803C>G0.299
embB4248319c.1806A>G0.278
embB4248322c.1809G>A0.280
ethA4326230p.Asp415Gly1.000
gid4407588c.615T>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
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;