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: 5de50fd30560f
Sample: 5de50fd30560f

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Summary
ID: 5de50fd30560f
Date: Mon Dec 2 13:24:25 2019
Strain: lineage3;lineage4.1.1;lineage1.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.Leu359Ile (0.13)
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage3East-African-IndianCASRD750
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage1.2.2Indo-OceanicEAI1RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6196c.957C>T0.119
gyrB6268c.1029C>G0.132
gyrB6280c.1041T>C0.137
gyrB6286c.1047T>C0.127
gyrB6289c.1050C>T0.127
gyrB6292c.1053G>C0.127
gyrB6307c.1068T>G0.150
gyrB6319c.1080G>C0.155
gyrB6346c.1107C>T0.178
gyrB6362c.1123T>C0.118
gyrB6655c.1416T>C0.117
gyrB6670c.1431G>C0.114
gyrB6673c.1434A>C0.114
gyrB6700c.1461T>C0.115
gyrB6709c.1470A>G0.117
gyrB6712c.1473G>C0.121
gyrB6728c.1489C>T0.128
gyrB6742c.1503A>G0.141
gyrB6745c.1506T>G0.140
gyrB6751c.1512G>C0.160
gyrB6760c.1521G>C0.168
gyrB6763c.1524G>C0.170
gyrB6775c.1536G>C0.174
gyrB6793c.1554T>C0.172
gyrB6797p.Gly520Thr0.176
gyrB6811c.1572C>T0.174
gyrB6841c.1602T>C0.203
gyrB6844c.1605T>C0.192
gyrB6853c.1614A>G0.139
gyrB6856c.1617T>C0.141
gyrB6859c.1620T>C0.139
gyrB6862c.1623C>G0.149
gyrB6868c.1629G>C0.143
gyrB7165c.1926C>G0.114
gyrB7178c.1939T>C0.115
gyrB7186c.1947C>G0.114
gyrB7246c.2007T>C0.115
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA7763c.462T>C0.157
gyrA7775c.474C>A0.157
gyrA7781c.480G>C0.131
gyrA7784c.483A>G0.125
gyrA7790c.489G>C0.121
gyrA7793c.492G>C0.121
gyrA7796c.495G>C0.127
gyrA7799c.498A>G0.132
gyrA7814c.513C>G0.121
gyrA7823c.522G>C0.124
gyrA7835c.534A>C0.129
gyrA7853c.552C>G0.138
gyrA7859c.558A>G0.136
gyrA7865c.564T>C0.130
gyrA7886c.585T>C0.131
gyrA8111c.810G>C0.127
gyrA8121c.820T>C0.140
gyrA8129c.828T>C0.144
gyrA8135c.834C>G0.147
gyrA8156c.855T>C0.148
gyrA8164p.Ala288Asp0.850
gyrA8168c.867A>G0.133
gyrA8177c.876A>C0.136
gyrA8198c.897T>C0.149
gyrA8207c.906T>C0.150
gyrA8219c.918T>C0.160
gyrA8225c.924T>C0.170
gyrA8234c.933T>C0.157
gyrA8237c.936A>G0.159
gyrA8247p.Ile316Val0.150
gyrA8264c.963T>C0.153
gyrA8267c.966G>C0.156
gyrA8270c.969G>C0.144
gyrA8276c.975G>A0.150
gyrA8283p.Ile328Leu0.136
gyrA8288c.987T>C0.136
gyrA8294c.993T>C0.208
gyrA8324c.1023T>C0.222
gyrA8330c.1029C>G0.246
gyrA8339c.1038A>G0.238
gyrA8340p.Ala347Ser0.238
gyrA8372c.1071G>C0.239
gyrA8375c.1074G>C0.227
gyrA8382p.Leu361Met0.214
gyrA8387c.1086C>T0.198
gyrA8391p.Tyr364His0.193
gyrA8399c.1098T>G0.200
gyrA8401p.Asp367Ala0.198
gyrA8405c.1104C>T0.198
gyrA8420c.1119T>C0.212
gyrA8442c.1141C>T0.223
gyrA8453c.1152A>C0.225
gyrA8459c.1158G>A0.208
gyrA8462c.1161A>T0.204
gyrA8465c.1164C>G0.202
gyrA8471c.1170T>C0.179
gyrA8472c.1171C>T0.179
gyrA8480c.1179C>A0.198
gyrA8486c.1185T>C0.191
gyrA8504c.1203G>C0.189
gyrA8516c.1215T>C0.160
gyrA8519c.1218A>C0.163
gyrA8520c.1219C>T0.165
gyrA8528c.1227G>C0.172
gyrA8543c.1242C>G0.194
gyrA8546c.1245T>C0.186
gyrA8552c.1251C>A0.190
gyrA8561c.1260A>G0.155
gyrA8576c.1275C>G0.146
gyrA8579c.1278C>T0.137
gyrA8588c.1287G>A0.131
gyrA8597c.1296C>G0.119
gyrA8603c.1302A>G0.119
gyrA8636c.1335A>C0.136
gyrA8642c.1341A>G0.135
gyrA8693c.1392T>C0.127
gyrA8696c.1395G>C0.125
gyrA8699c.1398A>G0.124
gyrA8711c.1410A>C0.136
gyrA8714c.1413A>G0.136
gyrA8729c.1428T>C0.126
gyrA8730p.Gly477Arg0.124
gyrA8740p.Arg480His0.126
gyrA8780p.Asp493Glu0.168
gyrA8786c.1485T>C0.172
gyrA8801c.1500G>C0.195
gyrA8807c.1506C>T0.200
gyrA8810c.1509A>G0.195
gyrA8816c.1515C>G0.189
gyrA8818p.Ser506Asn0.189
gyrA8828c.1527T>C0.208
gyrA8837c.1536C>T0.221
gyrA8852c.1551T>C0.213
gyrA8858c.1557T>C0.230
gyrA8867c.1566A>G0.220
gyrA8870c.1569G>C0.208
gyrA8873c.1572A>C0.215
gyrA8891c.1590G>A0.221
gyrA8897c.1596T>C0.221
gyrA8903c.1602T>C0.232
gyrA8933c.1632G>C0.203
gyrA8939c.1638T>C0.162
gyrA8942c.1641G>C0.164
gyrA8946c.1645T>C0.166
gyrA8966c.1665C>G0.178
gyrA8967p.Ala556Arg0.177
gyrA8987c.1686C>G0.176
gyrA8990c.1689C>G0.164
gyrA8996c.1695T>C0.173
gyrA8998p.Leu566Trp0.175
gyrA9017c.1716C>G0.172
gyrA9023c.1722A>C0.163
gyrA9029c.1728T>C0.148
gyrA9032c.1731T>C0.143
gyrA9035c.1734G>C0.137
gyrA9050p.Asp583Glu0.150
gyrA9051c.1750T>C0.144
gyrA9056c.1755C>G0.144
gyrA9062c.1761C>G0.145
gyrA9068c.1767G>C0.143
gyrA9071c.1770G>C0.136
gyrA9080c.1779G>T0.164
gyrA9089c.1788G>C0.164
gyrA9099c.1798T>C0.158
gyrA9104c.1803C>G0.158
gyrA9119c.1818A>G0.185
gyrA9122c.1821C>G0.185
gyrA9143c.1842T>C0.196
gyrA9152c.1851C>T0.175
gyrA9153p.Thr618Glu0.175
gyrA9158c.1857C>T0.179
gyrA9161c.1860C>G0.167
gyrA9182c.1881T>C0.194
gyrA9191c.1890G>C0.191
gyrA9200c.1899A>G0.179
gyrA9204p.Ser635Thr0.177
gyrA9224c.1923C>T0.168
gyrA9230c.1929T>C0.157
gyrA9233c.1932C>G0.157
gyrA9239c.1938C>T0.173
gyrA9252p.Val651Ile0.153
gyrA9284c.1983T>C0.169
gyrA9291c.1990C>T0.132
gyrA9296c.1995T>C0.126
gyrA9299c.1998G>C0.124
gyrA9300p.Ala667Ser0.123
gyrA9304p.Gly668Asp1.000
gyrA9308p.Asp669Glu0.122
gyrA9323c.2022C>G0.149
gyrA9335c.2034G>C0.161
gyrA9365c.2064G>A0.161
gyrA9374c.2073G>C0.161
gyrA9377c.2076A>G0.164
gyrA9383c.2082T>G0.157
gyrA9386c.2085T>C0.154
gyrA9395c.2094G>C0.138
gyrA9398c.2097T>C0.135
gyrA9413c.2112G>C0.136
gyrA9518c.2217A>G0.129
gyrA9602c.2301T>C0.159
gyrA9611p.Asp770Glu0.169
gyrA9626c.2325T>C0.147
gyrA9629c.2328C>G0.154
gyrA9630p.Val777Ile0.154
gyrA9635c.2334T>C0.152
gyrA9638c.2337C>G0.152
gyrA9641c.2340C>A0.151
gyrA9644c.2343T>C0.152
gyrA9650c.2349G>C0.182
gyrA9656c.2355C>G0.183
gyrA9665c.2364A>C0.183
gyrA9666p.Arg789Gly0.178
gyrA9674c.2373T>C0.188
gyrA9704c.2403T>G0.166
gyrA9708c.2407T>C0.162
gyrA9716c.2415T>C0.158
gyrA9725c.2424G>A0.149
gyrA9727p.Gly809Glu0.146
gyrA9729p.Asp810Asn0.146
gyrA9734c.2433A>C0.141
gyrA9749c.2448G>C0.142
gyrA9755c.2454C>T0.137
rpoB759606c.-201T>C0.260
rpoB759629c.-178T>C0.141
rpoB759746c.-61C>T0.933
rpoB759812c.6A>T0.112
rpoB760424c.618C>G0.124
rpoB760430c.624T>C0.136
rpoB760472c.666C>T0.158
rpoB760475c.669A>G0.157
rpoB760481c.675G>C0.155
rpoB760484c.678A>G0.158
rpoB760793c.987A>G0.141
rpoB760805c.999G>C0.141
rpoB760931c.1125C>G0.129
rpoB760934c.1128C>T0.128
rpoB760946c.1140A>G0.165
rpoB760982c.1176G>C0.168
rpoB760985c.1179G>C0.176
rpoB760991c.1185G>C0.185
rpoB761006c.1200C>G0.178
rpoB761015c.1209G>C0.165
rpoB761021c.1215G>C0.153
rpoB761027c.1221A>G0.163
rpoB761036c.1230G>C0.167
rpoB761037c.1231T>C0.167
rpoB761057c.1251G>C0.170
rpoB761102c.1296A>G0.163
rpoB761579c.1773G>C0.126
rpoB761588c.1782C>T0.134
rpoB761606c.1800C>G0.165
rpoB761612c.1806G>C0.167
rpoB761615c.1809A>C0.171
rpoB761636c.1830G>T0.211
rpoB761645c.1839C>G0.194
rpoB761648c.1842T>C0.179
rpoB761657c.1851C>G0.194
rpoB761675c.1869G>C0.204
rpoB761720c.1914C>G0.155
rpoB761725p.Glu640Ala0.149
rpoB761732c.1926C>G0.150
rpoB761735c.1929C>G0.150
rpoB761747c.1941G>C0.171
rpoB761750c.1944G>C0.176
rpoB761765c.1959T>C0.168
rpoB761772p.His656Ala0.164
rpoB761778p.Asn658Asp0.169
rpoB761791p.Arg662His0.142
rpoB761813c.2007T>C0.140
rpoB761815p.Ala670Glu0.140
rpoB761834c.2028T>C0.132
rpoB761848p.Cys681Ser0.114
rpoB761852c.2046C>G0.114
rpoB761858c.2052G>C0.116
rpoB761873c.2067A>C0.124
rpoB761885c.2079T>C0.126
rpoB761906c.2100C>G0.119
rpoB761912c.2106T>C0.123
rpoB761915p.Asp703Glu0.127
rpoB761916p.Asp704Asn0.127
rpoB761948c.2142G>C0.160
rpoB761954c.2148C>G0.148
rpoB762008c.2202C>T0.161
rpoB762014c.2208C>T0.144
rpoB762017c.2211A>G0.147
rpoB762083c.2277T>C0.125
rpoB762086c.2280G>C0.128
rpoB762101c.2295C>G0.143
rpoB762114p.Ile770Val0.154
rpoB762131c.2325C>G0.136
rpoB762140c.2334G>C0.148
rpoB762143c.2337T>C0.146
rpoB762149c.2343G>C0.153
rpoB762167c.2361T>C0.163
rpoB762176c.2370T>C0.162
rpoB762185c.2379G>C0.167
rpoB762206c.2400C>G0.164
rpoB762233c.2427G>C0.192
rpoB762246c.2440C>T0.178
rpoB762254c.2448T>G0.185
rpoB762257c.2451C>G0.186
rpoB762266c.2460T>C0.178
rpoB762284c.2478G>C0.189
rpoB762293c.2487T>C0.171
rpoB762314c.2508C>T0.160
rpoB762317c.2511A>G0.156
rpoB762329c.2523G>C0.136
rpoB762338c.2532T>C0.130
rpoB762347c.2541T>C0.142
rpoB762362p.Glu852Asp0.139
rpoB762369c.2563T>C0.142
rpoB762410c.2604T>G0.113
rpoB762419c.2613C>G0.115
rpoB762434c.2628T>G0.153
rpoB762449c.2643C>A0.151
rpoB762467c.2661C>T0.156
rpoB762488c.2682G>C0.113
rpoB762929c.3123G>C0.138
rpoB762989c.3183G>C0.186
rpoB762995c.3189G>T0.188
rpoB763013c.3207C>G0.191
rpoB763028c.3222T>C0.177
rpoB763031c.3225T>C0.177
rpoB763034c.3228C>G0.212
rpoB763040c.3234C>G0.228
rpoB763067c.3261C>G0.256
rpoB763070c.3264T>C0.256
rpoB763085c.3279C>G0.293
rpoB763115c.3309T>C0.269
rpoB763136c.3330C>T0.235
rpoB763148c.3342G>C0.200
rpoB763158c.3352C>T0.216
rpoB763166c.3360A>G0.222
rpoB763190c.3384C>T0.220
rpoB763214c.3408T>C0.140
rpoB763226c.3420A>G0.138
rpoB763227c.3421C>T0.148
rpoB763238c.3432T>C0.153
rpoB763253c.3447G>C0.146
rpoB763256c.3450G>A0.146
rpoB763268c.3462C>G0.148
rpoB763283c.3477T>C0.122
rpoB763284c.3478C>T0.123
rpoC763402c.33C>G0.120
rpoC763546c.177A>G0.118
rpoC763636c.267T>C0.139
rpoC763657c.288G>A0.155
rpoC763660c.291T>G0.155
rpoC763675c.306C>G0.143
rpoC763696c.327T>C0.153
rpoC763702c.333C>G0.165
rpoC763717c.348T>C0.174
rpoC763723c.354G>C0.177
rpoC763732c.363C>G0.184
rpoC763741c.372C>T0.176
rpoC763744c.375G>C0.174
rpoC763765c.396T>C0.174
rpoC763774c.405G>C0.191
rpoC763807c.438T>C0.132
rpoC763816c.447C>G0.138
rpoC763835p.Ala156Met0.157
rpoC763853p.Val162Ile0.184
rpoC763858c.489A>G0.186
rpoC763872p.Gly168Ala0.183
rpoC763876p.Glu169Asp0.187
rpoC763879c.510A>G0.194
rpoC763888c.519G>C0.196
rpoC763891c.522G>C0.194
rpoC763894c.525A>G0.191
rpoC763900c.531G>C0.198
rpoC763915c.546C>T0.242
rpoC763942c.573C>G0.253
rpoC763945c.576T>C0.250
rpoC763951c.582G>C0.253
rpoC763960c.591T>C0.235
rpoC763987c.618C>T0.253
rpoC763991p.Ile208Leu0.247
rpoC763996c.627T>C0.244
rpoC764002c.633C>G0.253
rpoC764005c.636G>C0.256
rpoC764020c.651C>T0.235
rpoC764024c.655T>C0.229
rpoC764032p.Asp221Glu0.189
rpoC764040p.Ser224Thr0.181
rpoC764044c.675T>C0.200
rpoC764059c.690G>T0.190
rpoC764083c.714A>G0.167
rpoC764098c.729A>G0.174
rpoC764101c.732C>G0.167
rpoC764102p.Val245Ile0.165
rpoC764112p.Tyr248Phe0.168
rpoC764116c.747C>T0.165
rpoC764131c.762T>C0.160
rpoC764248c.879C>G0.127
rpoC764266c.897T>C0.120
rpoC764269c.900G>C0.122
rpoC764272c.903G>C0.123
rpoC764278c.909A>G0.117
rpoC764338c.969G>A0.163
rpoC764353c.984G>C0.165
rpoC764365c.996C>T0.183
rpoC764380c.1011G>C0.145
rpoC764381c.1012T>A0.134
rpoC764387c.1018T>C0.138
rpoC764405c.1036A>C0.149
rpoC764419c.1050C>G0.154
rpoC764428c.1059G>C0.149
rpoC764431c.1062G>C0.147
rpoC764434c.1065A>G0.147
rpoC764446c.1077T>C0.158
rpoC764449c.1080G>C0.157
rpoC764452c.1083T>C0.168
rpoC764458c.1089G>C0.160
rpoC764461c.1092A>G0.162
rpoC764489c.1120C>T0.204
rpoC764497c.1128A>G0.194
rpoC764510c.1141C>T0.161
rpoC764521c.1152T>C0.150
rpoC764527c.1158C>T0.153
rpoC764536c.1167G>C0.153
rpoC764539c.1170C>G0.155
rpoC764548c.1179G>A0.149
rpoC764551c.1182G>C0.130
rpoC764764c.1395T>C0.120
rpoC764809c.1440C>T0.123
rpoC764827c.1458G>C0.130
rpoC765103c.1734G>T0.132
rpoC765292c.1923G>C0.132
rpoC765298c.1929G>C0.139
rpoC765300p.Val644Ala0.138
rpoC765319c.1950A>G0.149
rpoC765326p.His653Ala0.152
rpoC765330p.Ser654Asn0.152
rpoC765346c.1977C>G0.164
rpoC765349c.1980T>C0.157
rpoC765352c.1983G>C0.158
rpoC765364c.1995G>A0.126
rpoC765529c.2160C>T0.120
rpoC765541c.2172C>G0.128
rpoC765580c.2211G>C0.108
rpoC765734c.2365T>C0.128
rpoC765739c.2370G>T0.121
rpoC765751c.2382C>G0.115
rpoC765753p.Asp795Ala0.124
rpoC765772c.2403C>G0.125
rpoC765784c.2415C>G0.143
rpoC765787c.2418C>T0.152
rpoC765793c.2424C>G0.150
rpoC765796c.2427C>T0.150
rpoC765811c.2442T>C0.135
rpoC765814c.2445A>G0.133
rpoC765826c.2457T>C0.128
rpoC765835c.2466C>T0.126
rpoC765850c.2481G>C0.150
rpoC765883c.2514C>G0.154
rpoC765886c.2517C>G0.161
rpoC765892c.2523T>C0.164
rpoC766408c.3039C>G0.121
rpoC766411c.3042C>G0.121
rpoC766447c.3078T>C0.120
rpoC766492c.3123T>C0.118
rpoC766657c.3288A>G0.133
rpoC766672c.3303T>C0.128
rpoC766673p.Gly1102Asn0.128
rpoC766765c.3396A>C0.147
rpoC766774c.3405T>C0.144
rpoC766795c.3426C>T0.193
rpoC766801c.3432C>G0.196
rpoC766804c.3435A>G0.217
rpoC766861c.3492G>C0.258
rpoC766864c.3495G>C0.258
rpoC766900c.3531T>C0.287
rpoC766933c.3564A>G0.286
rpoC766945c.3576A>G0.299
rpoC766963c.3594T>C0.245
rpoC766972c.3603G>C0.270
rpoC766996c.3627C>T0.253
rpoC767009c.3640T>A0.222
rpoC767014c.3645G>C0.213
rpoC767033c.3664T>A0.222
rpoC767059c.3690T>G0.206
rpoC767062c.3693C>A0.189
rpoC767098c.3729T>C0.178
rpoC767119c.3750A>G0.162
rpoC767134c.3765C>A0.143
rpoC767158c.3789T>C0.121
rpoC767180p.Ala1271Gln0.163
rpoC767191c.3822C>G0.170
rpoC767206c.3837C>G0.151
rpoC767209c.3840T>C0.159
rpoC767212c.3843G>C0.155
rpoC767221c.3852C>G0.193
rpoC767230c.3861G>C0.182
rpoC767233c.3864T>C0.186
rpoC767263c.3894T>C0.171
rpoC767264p.Ala1299Gln0.159
rpoC767275c.3906T>C0.165
rpoC767278c.3909T>C0.167
rpoC767281c.3912C>G0.169
rpoC767284c.3915C>T0.171
rpoC767288c.3919C>T0.173
rpsL781348c.-212C>G0.146
rpsL781353c.-207T>C0.154
rpsL781373c.-187G>C0.154
rpsL781395c.-165T>C1.000
rpsL781571c.12C>T0.129
rpsL781628c.69T>C0.149
rpsL781631c.72G>C0.146
rpsL781649c.90T>C0.156
rpsL781655c.96T>C0.134
rpsL781700c.141G>C0.144
rpsL781703c.144G>T0.140
rpsL781715c.156T>C0.125
rpsL781728c.169T>C0.127
rpsL781736c.177T>C0.129
rpsL781742c.183C>T0.134
rpsL781748c.189C>G0.140
rpsL781754c.195G>C0.138
rpsL781760c.201T>C0.136
rpsL781772c.213C>A0.138
rpsL781808c.249C>T0.156
rpsL781811c.252C>T0.156
rpsL781832c.273T>C0.133
rpsL781838c.279G>C0.163
rpsL781841c.282C>G0.163
rpsL781865c.306G>C0.130
rpsL781868c.309T>C0.133
rpsL781871c.312G>C0.133
rpsL781877c.318T>C0.129
rpsL781892c.333A>G0.146
rpsL781898c.339A>T0.141
rpsL781916c.357T>C0.131
rpsL781929p.Gly124Ser0.123
rplC800814c.6A>G0.133
rplC800817c.9A>T0.133
rplC800844c.36T>C0.158
rplC801168c.360C>G0.116
rplC801171c.363A>G0.115
rplC801180c.372C>G0.120
rplC801195c.387G>C0.127
rplC801207c.399C>T0.124
rplC801255c.447C>T0.123
rplC801300c.492C>G0.139
rplC801309c.501C>G0.143
rplC801312c.504G>C0.142
rplC801321c.513C>T0.135
rplC801367p.Ala187Thr0.118
embR1416222p.Phe376Leu0.200
embR1416234p.Cys372Gly0.213
rrs1471923r.78t>c0.130
rrs1471925r.80t>c0.130
rrs1471932r.87a>g0.130
rrs1471934r.89a>g0.130
rrs1471969r.124t>c0.185
rrs1471970r.125g>a0.185
rrs1472075r.230a>g0.135
rrs1473105r.1260g>a0.114
rrs1473123r.1278a>t0.127
rrs1473145r.1300c>t0.153
rrs1473166r.1321g>a0.179
rrs1473290r.1445c>t0.165
rrl1473658r.1t>a0.209
rrl1473659r.2t>a0.209
rrl1473668r.11c>t0.222
rrl1473677r.20c>g0.254
rrl1473756r.99g>a0.216
rrl1473758r.101g>t0.216
rrl1473806r.149c>t0.194
rrl1474093r.436g>t0.161
rrl1474099r.442g>a0.158
rrl1474103r.446a>t0.145
rrl1474140r.483c>t0.150
rrl1474151r.494c>t0.153
rrl1474181r.524c>t0.213
rrl1474249r.592g>t0.290
rrl1474291r.634tttcctctccggagga>t0.328
rrl1474308r.651g>t0.241
rrl1474310r.653t>g0.236
rrl1474356r.699t>c0.244
rrl1474362r.705a>g0.244
rrl1474376r.719t>c0.244
rrl1474427r.770a>c0.147
rrl1474429r.772g>c0.143
rrl1474432r.775c>g0.139
rrl1474639r.982g>a0.326
rrl1474794r.1137c>t0.236
rrl1474812r.1155g>a0.260
rrl1474823r.1166c>t0.234
rrl1474831r.1174a>g0.229
rrl1474904r.1247g>a0.282
rrl1474956r.1299c>t0.179
rrl1474960r.1303c>g0.179
rrl1474963r.1306g>t0.194
rrl1474964r.1307t>a0.194
rrl1474965r.1308g>c0.194
rrl1474970r.1313g>a0.200
rrl1475006r.1349a>t0.200
rrl1475061r.1404c>t0.159
rrl1475088r.1431a>t0.255
rrl1475199r.1542g>a0.273
rrl1475206r.1549c>t0.273
rrl1475209r.1552g>c0.273
rrl1475213r.1556c>t0.273
rrl1475249r.1592t>c0.271
rrl1475252r.1595c>t0.275
rrl1475266r.1609t>c0.244
rrl1475267r.1610g>a0.244
rrl1475275r.1618c>t0.229
rrl1475276r.1619t>c0.229
rrl1475291r.1634a>c0.239
rrl1475313r.1656g>a0.273
rrl1475315r.1658a>t0.273
rrl1475355r.1698c>t0.265
rrl1475369r.1712g>t0.280
rrl1475402r.1745c>t0.271
rrl1475419r.1762c>t0.282
rrl1475429r.1772g>a0.282
rrl1475436r.1779c>t0.297
rrl1475483r.1826c>t0.333
rrl1475505r.1848g>a0.387
rrl1475526r.1869c>a0.316
rrl1475589r.1932g>a0.778
rrl1475599r.1942a>g0.211
rrl1475608r.1951t>c0.238
rrl1475642r.1985t>c0.186
rrl1475657r.2000a>g0.184
rrl1475659r.2002g>t0.184
rrl1475881r.2224t>c0.425
rrl1475988r.2331a>g0.450
rrl1476031r.2374c>t0.318
rrl1476032r.2375c>a0.318
rrl1476033r.2376t>c0.318
rrl1476034r.2377c>a0.318
rrl1476045r.2388g>t0.304
rrl1476047r.2390g>t0.292
rrl1476048r.2391g>a0.292
rrl1476049r.2392c>t0.292
rrl1476086r.2429g>a0.324
rrl1476089r.2432t>c0.286
rrl1476095r.2438c>g0.256
rrl1476106r.2449a>t0.244
rrl1476115r.2458t>c0.262
rrl1476117r.2460g>c0.262
rrl1476214r.2557g>a0.190
rrl1476224r.2567a>g0.188
rrl1476281r.2624t>c0.220
rrl1476583r.2926g>a0.171
rrl1476584r.2927c>t0.171
rrl1476594r.2937c>t0.143
rrl1476597r.2940g>a0.140
rrl1476603r.2946g>a0.143
rrl1476608r.2951c>g0.128
rrl1476628r.2971t>a0.140
fabG11673657p.Thr73Lys0.125
fabG11673667c.228A>G0.123
fabG11673679c.240T>G0.145
fabG11673685c.246C>T0.156
fabG11673710p.Leu91Ile0.184
fabG11673716p.Ala93Lys0.182
fabG11673733p.Met98Ile0.224
fabG11673748c.309A>G0.164
fabG11673749p.Lys104Arg0.178
fabG11673758p.Lys107Glu0.184
fabG11673890p.Ala151Ser0.181
fabG11673901c.462A>G0.171
fabG11673905p.Ser156Ala0.162
fabG11673916c.477A>C0.155
fabG11673917p.Val160Leu0.153
fabG11673922c.483T>C0.178
fabG11673941p.Ala168Ser0.177
fabG11673946c.507C>G0.167
fabG11673955c.516G>C0.156
fabG11673961c.522A>C0.127
inhA1674624c.423A>C0.133
inhA1674630c.429C>G0.128
inhA1674822c.621C>G0.118
inhA1674828c.627G>A0.118
inhA1674846p.Ile215Met0.127
inhA1674870c.669T>C0.110
inhA1674942c.741T>G0.110
inhA1674960c.759C>G0.110
inhA1674966c.765T>G0.108
rpsA1833532c.-10A>C0.127
rpsA1833554p.Thr5Ala0.167
rpsA1833568c.27G>C0.177
rpsA1833589c.48A>T0.158
rpsA1833595c.54T>C0.153
rpsA1833661c.120A>G0.138
rpsA1833667c.126C>G0.144
rpsA1833748c.207C>G0.114
rpsA1833787c.246C>G0.119
rpsA1833790c.249T>C0.119
rpsA1833802c.261A>G0.123
rpsA1833811c.270G>T0.128
rpsA1833838c.297G>C0.136
rpsA1833841c.300C>G0.135
rpsA1833847c.306C>G0.129
rpsA1834177c.636A>C0.118
rpsA1834189c.648G>C0.126
rpsA1834195c.654G>C0.140
rpsA1834210c.669C>T0.151
rpsA1834222c.681T>C0.169
rpsA1834249c.708T>C0.123
rpsA1834261c.720A>G0.120
rpsA1834411c.870T>C0.127
rpsA1834417c.876G>C0.126
rpsA1834423c.882G>C0.123
rpsA1834435c.894G>C0.140
rpsA1834451c.910T>C0.143
rpsA1834465c.924T>C0.132
rpsA1834468c.927A>G0.143
rpsA1834489c.948T>C0.153
rpsA1834510c.969C>T0.149
rpsA1834513c.972C>G0.143
rpsA1834528c.987T>C0.165
rpsA1834540c.999G>C0.167
rpsA1834546c.1005T>C0.169
rpsA1834609c.1068T>C0.126
rpsA1834633c.1092A>G0.130
rpsA1834639c.1098T>C0.137
rpsA1834654p.Glu371Asp0.135
rpsA1834684c.1143C>T0.143
rpsA1834690c.1149T>C0.167
rpsA1834732c.1191T>C0.145
rpsA1834733p.Ala398Ser0.145
rpsA1834738c.1197A>G0.147
rpsA1834753c.1212T>C0.141
rpsA1834765p.Glu408Asp0.157
rpsA1834775p.Ala412Thr0.155
rpsA1834780c.1239A>G0.143
rpsA1834786c.1245A>G0.146
rpsA1834789c.1248T>C0.143
rpsA1834792c.1251G>C0.141
rpsA1834849c.1308C>G0.157
rpsA1834852c.1311C>G0.145
tlyA1917972c.33A>G1.000
tlyA1918236c.297A>C0.160
tlyA1918248c.309T>C0.147
tlyA1918251c.312T>G0.151
tlyA1918258p.His107Glu0.144
tlyA1918271p.Ala111Val0.143
tlyA1918275c.336T>C0.143
tlyA1918278c.339C>G0.141
tlyA1918310p.Asn124Ser0.148
tlyA1918315p.Pro126Ala0.150
tlyA1918323c.384G>C0.139
tlyA1918326c.387G>C0.144
tlyA1918330p.Leu131Val0.144
tlyA1918346p.Ala136Val0.152
tlyA1918352p.Gly138Asp0.152
tlyA1918356c.417C>G0.152
tlyA1918359c.420A>G0.158
tlyA1918362c.423G>C0.153
tlyA1918422c.483T>C0.141
tlyA1918425c.486C>A0.137
tlyA1918434c.495C>G0.122
katG2154724p.Arg463Leu1.000
katG2155179c.933G>A0.157
katG2155185c.927A>G0.164
katG2155190p.Thr308Ser0.149
katG2155191c.921T>A0.149
katG2155200c.912A>G0.187
pncA2289047c.195G>A1.000
kasA2518121p.Gln3Lys0.161
kasA2518132c.18C>T0.165
kasA2518138c.24T>C0.163
kasA2518174c.60A>G0.153
kasA2518190p.Ser26Ala0.188
kasA2518199p.Ile29Val0.176
kasA2518220c.106C>T0.174
kasA2518234c.120G>A0.159
kasA2518248p.Ala45Val0.157
kasA2518261p.Glu49Asp0.147
kasA2518263p.Phe50Tyr0.147
kasA2518265p.Val51Ile0.147
kasA2518413p.Ser100Asn0.143
kasA2518421p.Val103Leu0.138
kasA2518429c.315A>C0.128
kasA2518439p.Ala109Ser0.134
kasA2518444c.330T>C0.128
kasA2518447c.333T>G0.126
kasA2518459c.345T>C0.133
kasA2518462c.348A>C0.131
kasA2518468c.354A>C0.134
kasA2518474c.360G>A0.135
kasA2518480c.366T>C0.182
kasA2518483c.369C>G0.182
kasA2518504c.390T>C0.189
kasA2518506p.Ala131Glu0.186
kasA2518519c.405G>C0.189
kasA2518528c.414C>G0.187
kasA2518540c.426T>C0.183
kasA2518561c.447T>C0.190
kasA2518567c.453G>C0.152
kasA2518570c.456G>C0.152
kasA2518574p.Ile154Val0.158
kasA2518579c.465T>C0.154
kasA2518588c.474T>C0.167
kasA2518591c.477G>C0.165
kasA2518609p.Met165Ile0.165
kasA2518864c.750G>C0.126
kasA2518879c.765A>G0.138
kasA2518885c.771T>C0.140
kasA2518898c.784T>C0.135
kasA2518906c.792A>G0.135
kasA2518910p.Leu266Met0.137
kasA2518921c.807T>C0.127
kasA2518951c.837G>C0.111
kasA2519008c.894C>G0.125
kasA2519050c.936C>G0.137
kasA2519053c.939G>C0.137
kasA2519056c.942G>C0.133
kasA2519062c.948T>G0.197
kasA2519068c.954C>T0.190
kasA2519072p.Ala320Thr0.179
kasA2519107c.993T>C0.165
kasA2519108p.Asp332Gln0.165
kasA2519122c.1008G>C0.159
kasA2519137c.1023T>G0.163
kasA2519158c.1044C>T0.171
kasA2519167c.1053T>G0.175
kasA2519173c.1059C>G0.183
kasA2519196p.Thr361Ser0.176
ahpC2726105c.-88G>A1.000
ahpC2726210c.18T>C0.117
ahpC2726216c.24T>C0.132
ahpC2726219c.27A>G0.128
ahpC2726232p.Gln14Glu0.132
ahpC2726243c.51T>G0.127
ahpC2726244c.52C>T0.127
ahpC2726251p.Gly20Ala0.129
ahpC2726255c.63T>C0.130
ahpC2726258c.66C>T0.161
ahpC2726303c.111T>C0.213
ahpC2726311p.Ser40Asn0.186
ahpC2726315p.Asp41Glu0.191
ahpC2726318p.Glu42Asp0.194
ahpC2726322p.Pro44Ala0.191
ahpC2726330c.138G>A0.200
ahpC2726336c.144G>C0.200
ahpC2726348c.156T>C0.224
ahpC2726357c.165A>G0.246
ahpC2726366c.174G>C0.265
ahpC2726378c.186T>G0.208
ahpC2726387c.195C>T0.164
ahpC2726390c.198G>C0.167
ahpC2726393c.201G>C0.157
ahpC2726397p.Ser69Gly0.153
ahpC2726408c.216T>C0.141
ahpC2726414c.222G>A0.125
ahpC2726420p.Glu76Asp0.125
ahpC2726493p.Asn101Glu0.118
ahpC2726506p.Thr105Lys0.125
ahpC2726508c.316T>C0.123
ahpC2726528c.336C>G0.113
ahpC2726540c.348C>G0.118
ahpC2726543c.351A>G0.114
ahpC2726546c.354C>G0.115
ahpC2726551p.Gln120Leu0.122
ahpC2726556p.Ala122Thr0.117
ahpC2726564c.372C>G0.143
ahpC2726591c.399C>G0.131
ahpC2726593p.Val134Ala0.133
ahpC2726600c.408T>C0.135
ahpC2726601p.Ile137Leu0.135
folC2747289p.Pro104Ala0.118
folC2747290c.309T>C0.119
folC2747293c.306C>T0.116
folC2747302c.297T>C0.133
folC2747314c.285T>G0.143
folC2747317c.282G>C0.136
folC2747343p.Val86Ile0.129
folC2747355p.Val82Ile0.131
folC2747359c.240G>C0.135
folC2747362c.237C>G0.135
folC2747394p.Ile69Val0.132
folC2747395c.204A>G0.128
folC2747407c.192A>G0.111
folC2747415p.Arg62Cys0.115
folC2747419c.180G>C0.119
folC2747422c.177C>T0.120
folC2747425c.174G>A0.116
folC2747442c.157A>G0.189
folC2747467p.Asp44Glu0.156
ribD2987066c.228A>G0.114
ribD2987069c.231T>C0.115
ribD2987092p.Val85Ala0.110
thyX3067286c.660G>C0.133
thyX3067289c.657G>C0.130
thyX3067292c.654C>T0.128
thyX3067295c.651G>A0.128
thyX3067313c.633C>A0.196
thyX3067316c.630T>C0.196
thyX3067325c.621T>C0.212
thyX3067349c.597C>G0.211
thyX3067355c.591T>G0.215
thyX3067367c.579C>G0.228
thyX3067373c.573G>C0.221
thyX3067391c.555C>G0.183
thyX3067394c.552C>G0.177
thyX3067439c.507T>C0.172
thyX3067442c.504G>A0.172
thyX3067445c.501G>C0.165
thyX3067457c.489G>C0.154
thyX3067462c.484G>A0.148
thyX3067465p.Ile161Val0.154
thyX3067466c.480C>G0.157
thyX3067475c.471T>C0.148
thyX3067490c.456G>C0.142
thyX3067493c.453T>C0.140
thyX3067510c.436G>A0.144
thyX3067515p.Ser144Thr0.145
thyX3067531p.Ala139Ser0.128
thyX3067545p.Glu134Ala0.127
thyX3067549p.Thr133Ala0.124
thyX3067556p.His130Gln0.142
thyX3067559c.387G>C0.139
thyX3067565p.Asp127Glu0.157
thyX3067570p.Ala126Pro0.160
thyX3067577c.369C>T0.154
thyX3067602p.Arg115His0.155
thyX3067611p.Lys112Thr0.133
thyX3067619c.327T>G0.136
thyX3067631c.315G>C0.170
thyX3067634c.312G>C0.170
thyX3067637c.309C>T0.174
thyX3067652c.294A>G0.194
thyX3067661c.285G>C0.200
thyX3067685c.261T>G0.190
thyX3067693p.Ile85Leu0.172
thyX3067694c.252C>G0.172
thyX3067718c.228G>C0.191
thyX3067721c.225A>G0.193
thyX3067727c.219T>G0.150
thyX3067736c.210G>A0.158
thyX3067762p.Arg62Lys0.139
thyX3067765p.Leu61Ile0.139
thyX3067772c.174G>C0.141
thyX3067775c.171G>A0.140
thyX3067781c.165G>C0.149
thyX3067793c.153A>G0.157
thyX3067799c.147C>T0.153
thyX3067802c.144G>C0.157
thyX3067814c.132A>G0.146
thyX3067850c.96T>G0.120
ald3086788c.-32T>C0.989
ald3087578c.759A>C0.132
ald3087590p.His257Gln0.125
ald3087599c.780A>G0.130
ald3087602c.783T>C0.130
ald3087608c.789A>G0.125
ald3087614c.795G>C0.125
ald3087617c.798T>C0.125
ald3087620c.801A>C0.129
ald3087623c.804C>G0.140
ald3087641c.822T>C0.195
ald3087647c.828A>G0.177
ald3087649p.Gly277Asp0.171
ald3087653c.834A>G0.169
ald3087656c.837A>G0.171
ald3087665c.846C>G0.177
ald3087666p.Tyr283His0.176
ald3087672p.His285Asp0.189
ald3087680c.861G>C0.200
ald3087704c.885T>C0.182
ald3087716c.897G>C0.187
ald3087726p.Ala303Ser0.171
ald3087729p.Ser304Ala0.167
ald3087737c.918G>C0.158
ald3087749c.930C>G0.148
ald3087750p.Tyr311Val0.150
ald3087761c.942C>G0.161
ald3087770c.951G>C0.158
ald3087787p.Glu323Ala0.131
ald3087791c.972T>C0.136
ald3087797p.Asp326Glu0.121
ald3087799p.His327Arg0.123
ald3087809c.990G>T0.128
fbiA3640347c.-196A>G0.135
fbiA3640349c.-194A>G0.135
fbiA3640350c.-193C>T0.144
fbiA3640365c.-178C>G0.161
alr3840215c.1206A>G0.168
alr3840230c.1191A>C0.183
alr3840233c.1188T>C0.182
alr3840236c.1185T>G0.186
alr3840239c.1182C>G0.186
alr3840248c.1173G>C0.182
alr3840482c.939A>T1.000
alr3841473c.-53G>A1.000
alr3841652c.-232A>T0.252
alr3841654c.-234A>C0.261
alr3841662c.-242A>G0.326
alr3841663c.-243G>A0.296
embC4240512p.Ser217Thr0.126
embC4240516c.654G>C0.126
embC4240519c.657T>C0.125
embC4240543c.681G>C0.129
embC4240651c.789G>A0.143
embC4240726c.864G>C0.147
embC4240780c.918T>C0.168
embC4240783c.921G>C0.170
embC4240789c.927T>C0.160
embC4240819c.957A>G0.167
embC4240828c.966G>A0.165
embC4240831c.969T>G0.150
embC4240867c.1005T>C0.134
embC4240870c.1008T>C0.133
embC4240873c.1011C>G0.131
embC4240879c.1017G>C0.132
embC4240880p.Ala340Thr0.132
embC4240885c.1023T>C0.124
embC4240897c.1035C>G0.117
embC4240945c.1083T>G0.120
embC4240954p.Ile364Met0.114
embC4240960c.1098G>C0.116
embC4241089c.1227C>G0.130
embC4241095c.1233C>T0.143
embC4241107c.1245G>C0.130
embC4241140c.1278A>G0.150
embC4241146c.1284C>G0.167
embC4241158c.1296T>C0.167
embC4241161c.1299C>G0.168
embC4241162c.1300T>C0.170
embC4241170c.1308G>C0.167
embC4241173c.1311C>T0.163
embC4241203c.1341T>C0.156
embC4241206c.1344G>C0.155
embC4241218c.1356G>C0.176
embC4241230c.1368A>G0.158
embC4241233c.1371G>C0.151
embC4241318p.Pro486Thr0.988
embC4241449c.1587C>G0.190
embC4241453p.Ile531Val0.185
embC4241479c.1617C>G0.202
embC4241480c.1618T>C0.202
embC4241488c.1626G>C0.211
embC4241496p.Ala545Gly0.189
embC4241500c.1638A>C0.191
embC4241501p.Ser547Thr0.191
embC4241506c.1644G>C0.209
embC4241518c.1656A>G0.211
embC4241521c.1659T>C0.213
embC4241530c.1668C>G0.219
embC4241536c.1674A>G0.213
embC4241539c.1677T>C0.213
embC4241545c.1683T>C0.208
embC4241548c.1686T>C0.211
embC4241551c.1689A>G0.208
embC4241567p.Ile569Val0.247
embC4241572c.1710C>G0.250
embC4241578c.1716G>C0.247
embC4241584c.1722T>C0.247
embC4241587c.1725C>G0.247
embC4241591p.Leu577Val0.263
embC4241611c.1749G>C0.304
embC4241614c.1752A>C0.304
embC4241626c.1764T>C0.329
embC4241635c.1773G>C0.329
embC4241644c.1782G>C0.299
embC4241648c.1786T>C0.294
embC4241657p.Ser599Pro0.323
embC4241665c.1803G>C0.313
embC4241671c.1809T>C0.318
embC4241689c.1827G>C0.172
embC4241691p.Gly610Ala0.169
embC4241694p.Ala611Val0.164
embC4241698c.1836G>C0.169
embC4241704c.1842C>G0.169
embC4241707c.1845G>A0.179
embC4241713c.1851G>C0.215
embC4241719c.1857G>C0.212
embC4241727p.Phe622Tyr0.274
embC4241741p.Val627Leu0.244
embC4241747p.Val629Leu0.241
embC4241750p.Leu630Val0.241
embC4241755c.1893C>G0.256
embC4241770c.1908T>C0.276
embC4241791c.1929G>C0.256
embC4241794c.1932C>G0.259
embC4241797c.1935C>T0.259
embC4241809c.1947A>C0.250
embC4241995c.2133C>G0.218
embC4242002p.Leu714Val0.203
embC4242007c.2145G>A0.211
embC4242011p.Leu717Val0.211
embC4242024p.Val721Ala0.193
embC4242036p.Gln725Leu0.195
embC4242045p.Ile728Thr0.118
embC4242055c.2193C>T0.149
embC4242061c.2199G>C0.155
embC4242070c.2208T>C0.146
embC4242075p.Arg738His0.851
embC4242079c.2217T>C0.151
embC4242085c.2223A>G0.157
embC4242091c.2229T>G0.160
embC4242092c.2230T>C0.160
embC4242095p.Ala745Thr0.169
embC4242106c.2244C>G0.195
embC4242121c.2259A>G0.179
embC4242138p.Leu759Gln0.160
embC4242142c.2280T>C0.160
embC4242145c.2283C>G0.160
embC4242151c.2289A>G0.160
embC4242160c.2298G>C0.123
embC4242161p.Ala767Ser0.122
embC4242170p.Thr770Gly0.120
embC4242175c.2313G>C0.123
embC4242176p.Pro772Ser0.123
embC4242179p.Leu773Ala0.123
embC4242184c.2322C>G0.123
embC4242193c.2331G>C0.145
embC4242196c.2334A>C0.145
embC4242208c.2346T>G0.156
embC4242220c.2358A>G0.167
embC4242229c.2367C>A0.158
embC4242245p.Thr795Arg0.129
embC4242519p.Thr886Ser0.121
embC4242532c.2670A>T0.162
embC4242539p.Ser893Pro0.159
embC4242544c.2682C>T0.171
embC4242552p.Arg897Gln0.176
embC4242554p.Leu898Val0.173
embC4242577c.2715A>G0.178
embC4242585p.Ala908Gly0.151
embC4242589c.2727A>G0.137
embC4242594p.His911Pro0.133
embC4242598c.2736T>C0.118
embC4242601c.2739G>C0.113
embC4242607p.Met915Ile0.113
embC4242608p.Glu916Gln0.113
embC4242631c.2769G>C0.114
embC4242643c.2781C>T0.892
embC4242689p.Val943Ile0.156
embC4242710p.Gln950Glu0.175
embC4242715c.2853T>C0.174
embC4242742c.2880C>G0.152
embC4242748c.2886A>G0.161
embC4242754c.2892G>C0.159
embC4242764p.Val968Leu0.145
embC4242772c.2910G>C0.151
embC4242779p.Asn973Asp0.132
embA4244366c.1134C>G0.159
embA4244372c.1140T>G0.169
embA4244378c.1146G>A0.157
embA4244381c.1149G>A0.148
embA4244390c.1158G>C0.136
embA4244393c.1161G>C0.122
embA4244396c.1164T>C0.121
embA4244408c.1176G>C0.118
embA4244523p.Pro431Ala0.125
embA4244534c.1302T>C0.136
embA4244537c.1305T>G0.136
embA4244543c.1311C>G0.140
embA4244547p.Ile439Val0.133
embA4244582c.1350T>C0.118
embA4244585c.1353A>G0.119
embA4244670p.Ala480Leu0.118
embA4244675c.1443A>G0.118
embA4244678c.1446G>C0.117
embA4244681c.1449A>C0.128
embA4244690c.1458G>A0.148
embA4244702c.1470C>G0.155
embA4244708c.1476C>G0.153
embA4244728p.Phe499Trp0.147
embA4245041c.1809C>G0.120
embA4245044c.1812G>C0.120
embA4245053c.1821G>C0.144
embA4245060c.1828T>C0.152
embA4245083c.1851A>C0.189
embA4245089c.1857G>C0.179
embA4245101c.1869G>C0.173
embA4245137c.1905T>C0.200
embA4245146c.1914G>A0.194
embA4245149c.1917C>G0.186
embA4245153p.Ile641Val0.184
embA4245182c.1950T>C0.180
embA4245189c.1957C>T0.182
embA4245198p.Leu656Ile0.204
embA4245207c.1975T>C0.200
embA4245215c.1983A>C0.204
embA4245222p.Tyr664Gln0.194
embA4245248c.2016G>C0.178
embA4245257c.2025A>G0.184
embA4245263c.2031A>G0.188
embA4245282p.Ile684Val0.176
embA4245285c.2053T>C0.168
embA4245290c.2058C>G0.162
embA4245293c.2061T>G0.162
embA4245296c.2064G>C0.160
embA4245299c.2067A>G0.162
embA4245431c.2199T>C0.119
embA4245434c.2202G>C0.119
embA4245470c.2238T>C0.147
embA4245473c.2241C>G0.149
embA4245483p.Gln751Ala0.112
embA4245490p.Val753Ala0.115
embA4245501p.Ala757Thr0.112
embA4245512c.2280G>C0.116
embA4245518c.2286A>G0.116
embA4245524c.2292G>C0.116
embA4245527c.2295C>G0.114
embA4245530c.2298T>C0.114
embA4245531p.Ile767Val0.114
embA4245535p.Ser768Asn0.118
embA4245539c.2307C>G0.130
embA4245542c.2310C>G0.133
embA4245557c.2325G>A0.203
embA4245575c.2343C>G0.192
embA4245576p.Lys782Gln0.192
embA4245659c.2427C>G0.158
embA4245674c.2442A>C0.205
embA4245677c.2445G>C0.203
embA4245693p.Ile821Val0.189
embA4245701c.2469G>C0.192
embA4245704c.2472G>C0.216
embA4245725c.2493A>G0.192
embA4245726c.2494T>C0.192
embA4245737c.2505A>C0.188
embA4245740c.2508T>C0.215
embA4245764c.2532G>C0.270
embA4245772p.Asn847Thr0.265
embA4245785c.2553G>C0.231
embA4245807c.2575T>C0.154
embA4245812c.2580G>C0.156
embA4245813p.Pro861Ala0.159
embA4245820p.Ser863Thr0.164
embA4245824c.2592G>C0.164
embA4245833c.2601G>C0.194
embA4245842c.2610G>C0.213
embA4245845c.2613T>C0.216
embA4245851c.2619G>C0.224
embA4245860c.2628C>G0.215
embA4245885p.Asp885Thr0.197
embA4245892p.Ile887Thr0.195
embA4245899c.2667C>G0.190
embA4245902c.2670G>A0.197
embA4245905c.2673C>G0.200
embA4245911c.2679A>G0.200
embA4245917c.2685G>A0.200
embA4245930p.Gly900Arg0.170
embA4246010c.2778G>T0.108
embA4246022c.2790C>G0.125
embA4246040c.2808C>G0.126
embA4246041p.Asp937Asn0.126
embA4246055c.2823T>C0.128
embA4246064c.2832T>C0.135
embA4246080p.Pro950Ser0.120
embA4246164c.2932T>C0.167
embA4246184c.2952A>C0.168
embA4246196c.2964C>G0.173
embA4246205c.2973A>G0.168
embA4246211c.2979T>C0.168
embA4246217c.2985G>A0.149
embA4246220c.2988T>C0.149
embA4246223c.2991C>T0.149
embA4246227p.Ile999Val0.151
embA4246235c.3003G>A0.196
embA4246242p.Gln1004Gly0.188
embA4246250c.3018G>C0.173
embA4246256c.3024G>T0.160
embA4246259c.3027G>C0.161
embA4246264p.His1011Arg0.144
embA4246292c.3060A>G0.128
embA4246329p.Thr1033Ala0.129
embA4246349c.3117C>G0.136
embB4246669c.156C>G0.140
embB4247464c.951C>G0.139
embB4247470c.957T>C0.141
embB4247491c.978G>C0.152
embB4247497c.984T>C0.175
embB4247512c.999T>C0.138
embB4247539c.1026T>C0.133
embB4247554c.1041T>C0.137
embB4247566c.1053C>A0.144
embB4247572c.1059A>G0.144
embB4247579p.Ala356Phe0.135
embB4247587c.1074G>A0.131
embB4247603c.1090C>T0.139
embB4247611c.1098G>T0.133
embB4247614c.1101T>C0.136
embB4247940p.Leu476Trp0.121
embB4247974c.1461C>G0.138
embB4248007c.1494C>G0.120
embB4248011p.Ser500Arg0.116
embB4248014p.Thr501Ala0.116
embB4248035p.Val508Ile0.123
embB4248040c.1527C>G0.126
embB4248041p.Ala510Thr0.125
embB4248044p.Lys511Ala0.125
embB4248070c.1557T>C0.175
embB4248085c.1572T>C0.177
embB4248097c.1584C>G0.172
embB4248130c.1617G>C0.163
embB4248142c.1629T>C0.159
embB4248143c.1630T>C0.157
embB4248157c.1644A>G0.193
embB4248172c.1659G>C0.206
embB4248199c.1686A>G0.172
embB4248200p.Ile563Val0.169
embB4248205c.1692C>G0.164
embB4248206p.Ser565Gly0.169
embB4248220c.1707A>C0.188
embB4248304c.1791G>C0.163
embB4248316c.1803C>G0.144
embB4248319c.1806A>G0.144
embB4248343c.1830G>C0.153
embB4248350c.1837T>C0.127
embB4248355c.1842A>G0.125
embB4248358c.1845C>G0.128
embB4248361c.1848A>C0.127
embB4248362p.Ser617Ala0.129
embB4248373c.1860C>G0.174
embB4248382c.1869C>G0.186
embB4248386c.1873C>A0.155
embB4248457c.1944T>C0.118
embB4248472c.1959T>C0.115
embB4248475c.1962G>C0.115
embB4248504p.Asp664Gly0.122
embB4248535c.2022C>G0.124
embB4249153c.2640G>C0.111
embB4249164p.Ala884Asp0.125
ethA4326307c.1167G>C0.172
ethA4326310c.1164A>G0.172
ethR4327746c.198A>G0.151
ethR4327755p.Glu69Asp0.154
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.

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