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comparison test-data/rif_resistant_variants_report.html @ 3:42818629ec4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
author iuc
date Fri, 31 May 2024 20:06:49 +0000
parents adc0645b945c
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2:4934c0ac6197 3:42818629ec4c
20 <h2 class="mt-5"> 20 <h2 class="mt-5">
21 rif_resistant Report 21 rif_resistant Report
22 </h2> 22 </h2>
23 </div> 23 </div>
24 <hr> 24 <hr>
25 <div> 25 <div class="row justify-content-center align-items-center">
26 <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html" 26 <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
27 target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p> 27 <thead class="thead-light">
28 <p>Kindly check if the '<strong>ANN</strong>' field is present.</p> 28 <tr>
29 <th scope="col">CHR</th>
30 <th scope="col">GENE</th>
31 <th scope="col">LOCUS</th>
32 <th scope="col">PRODUCT</th>
33 <th scope="col">IS_SNV</th>
34 <th scope="col">EFFECT</th>
35 <th scope="col">POS</th>
36 <th scope="col">REF</th>
37 <th scope="col">ALT</th>
38 <th scope="col">BIOTYPE</th>
39 <th scope="col">NUCLEOTIDE</th>
40 <th scope="col">CONSEQUENCE</th>
41 <th scope="col">IMPACT</th>
42 <th scope="col">PATHWAY</th>
43 </tr>
44 </thead>
45 <tbody>
46
47 <tr>
48 <td>Chromosome</td>
49 <td>Rv0014c</td>
50 <td>
51 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0014c" target="_blank"
52 rel="noreferrer noopener">GENE_Rv0014c</a>
53 </td>
54 <td>
55 <p>NA</p>
56 </td>
57 <td>True</td>
58 <td>synonymous_variant</td>
59 <td>
60 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A15890..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A15890..None"
61 target="_blank" rel="noreferrer noopener">15890</a>
62 </td>
63 <td>G</td>
64 <td>A</td>
65 <td>protein_coding</td>
66 <td>c.1581C>T</td>
67 <td>p.Ser527Ser</td>
68 <td>LOW</td>
69 <td>
70 <p>NA</p>
71 </td>
72 </tr>
73 <tr>
74 <td>Chromosome</td>
75 <td>Rv0127</td>
76 <td>
77 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0127" target="_blank"
78 rel="noreferrer noopener">GENE_Rv0127</a>
79 </td>
80 <td>
81 <p>NA</p>
82 </td>
83 <td>True</td>
84 <td>synonymous_variant</td>
85 <td>
86 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A154990..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A154990..None"
87 target="_blank" rel="noreferrer noopener">154990</a>
88 </td>
89 <td>G</td>
90 <td>T</td>
91 <td>protein_coding</td>
92 <td>c.759G>T</td>
93 <td>p.Arg253Arg</td>
94 <td>LOW</td>
95 <td>
96 <p>NA</p>
97 </td>
98 </tr>
99 <tr>
100 <td>Chromosome</td>
101 <td>Rv0284</td>
102 <td>
103 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0284" target="_blank"
104 rel="noreferrer noopener">GENE_Rv0284</a>
105 </td>
106 <td>
107 <p>NA</p>
108 </td>
109 <td>True</td>
110 <td>synonymous_variant</td>
111 <td>
112 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A346693..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A346693..None"
113 target="_blank" rel="noreferrer noopener">346693</a>
114 </td>
115 <td>G</td>
116 <td>T</td>
117 <td>protein_coding</td>
118 <td>c.1059G>T</td>
119 <td>p.Ser353Ser</td>
120 <td>LOW</td>
121 <td>
122 <p>NA</p>
123 </td>
124 </tr>
125 <tr>
126 <td>Chromosome</td>
127 <td>Rv0372c</td>
128 <td>
129 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0372c" target="_blank"
130 rel="noreferrer noopener">GENE_Rv0372c</a>
131 </td>
132 <td>
133 <p>NA</p>
134 </td>
135 <td>True</td>
136 <td>synonymous_variant</td>
137 <td>
138 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A449194..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A449194..None"
139 target="_blank" rel="noreferrer noopener">449194</a>
140 </td>
141 <td>G</td>
142 <td>A</td>
143 <td>protein_coding</td>
144 <td>c.192C>T</td>
145 <td>p.Gly64Gly</td>
146 <td>LOW</td>
147 <td>
148 <p>NA</p>
149 </td>
150 </tr>
151 <tr>
152 <td>Chromosome</td>
153 <td>Rv0411c</td>
154 <td>
155 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0411c" target="_blank"
156 rel="noreferrer noopener">GENE_Rv0411c</a>
157 </td>
158 <td>
159 <p>NA</p>
160 </td>
161 <td>True</td>
162 <td>synonymous_variant</td>
163 <td>
164 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A497491..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A497491..None"
165 target="_blank" rel="noreferrer noopener">497491</a>
166 </td>
167 <td>G</td>
168 <td>A</td>
169 <td>protein_coding</td>
170 <td>c.810C>T</td>
171 <td>p.Asp270Asp</td>
172 <td>LOW</td>
173 <td>
174 <p>NA</p>
175 </td>
176 </tr>
177 <tr>
178 <td>Chromosome</td>
179 <td>Rv0667</td>
180 <td>
181 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0667" target="_blank"
182 rel="noreferrer noopener">GENE_Rv0667</a>
183 </td>
184 <td>
185 <p>NA</p>
186 </td>
187 <td>True</td>
188 <td>missense_variant</td>
189 <td>
190 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A761110..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A761110..None"
191 target="_blank" rel="noreferrer noopener">761110</a>
192 </td>
193 <td>A</td>
194 <td>T</td>
195 <td>protein_coding</td>
196 <td>c.1304A>T</td>
197 <td>p.Asp435Val</td>
198 <td>MODERATE</td>
199 <td>
200 <p>NA</p>
201 </td>
202 </tr>
203 <tr>
204 <td>Chromosome</td>
205 <td>Rv0715</td>
206 <td>
207 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0715" target="_blank"
208 rel="noreferrer noopener">GENE_Rv0715</a>
209 </td>
210 <td>
211 <p>NA</p>
212 </td>
213 <td>True</td>
214 <td>synonymous_variant</td>
215 <td>
216 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A811753..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A811753..None"
217 target="_blank" rel="noreferrer noopener">811753</a>
218 </td>
219 <td>C</td>
220 <td>T</td>
221 <td>protein_coding</td>
222 <td>c.12C>T</td>
223 <td>p.His4His</td>
224 <td>LOW</td>
225 <td>
226 <p>NA</p>
227 </td>
228 </tr>
229 <tr>
230 <td>Chromosome</td>
231 <td>Rv1391</td>
232 <td>
233 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1391" target="_blank"
234 rel="noreferrer noopener">GENE_Rv1391</a>
235 </td>
236 <td>
237 <p>NA</p>
238 </td>
239 <td>True</td>
240 <td>synonymous_variant</td>
241 <td>
242 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1565566..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1565566..None"
243 target="_blank" rel="noreferrer noopener">1565566</a>
244 </td>
245 <td>C</td>
246 <td>T</td>
247 <td>protein_coding</td>
248 <td>c.126C>T</td>
249 <td>p.Pro42Pro</td>
250 <td>LOW</td>
251 <td>
252 <p>NA</p>
253 </td>
254 </tr>
255 <tr>
256 <td>Chromosome</td>
257 <td>Rv1630</td>
258 <td>
259 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1630" target="_blank"
260 rel="noreferrer noopener">GENE_Rv1630</a>
261 </td>
262 <td>
263 <p>NA</p>
264 </td>
265 <td>True</td>
266 <td>synonymous_variant</td>
267 <td>
268 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1834177..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1834177..None"
269 target="_blank" rel="noreferrer noopener">1834177</a>
270 </td>
271 <td>A</td>
272 <td>C</td>
273 <td>protein_coding</td>
274 <td>c.636A>C</td>
275 <td>p.Arg212Arg</td>
276 <td>LOW</td>
277 <td>
278 <p>NA</p>
279 </td>
280 </tr>
281 <tr>
282 <td>Chromosome</td>
283 <td>Rv1640c</td>
284 <td>
285 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1640c" target="_blank"
286 rel="noreferrer noopener">GENE_Rv1640c</a>
287 </td>
288 <td>
289 <p>NA</p>
290 </td>
291 <td>True</td>
292 <td>synonymous_variant</td>
293 <td>
294 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1849051..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1849051..None"
295 target="_blank" rel="noreferrer noopener">1849051</a>
296 </td>
297 <td>C</td>
298 <td>T</td>
299 <td>protein_coding</td>
300 <td>c.2985G>A</td>
301 <td>p.Pro995Pro</td>
302 <td>LOW</td>
303 <td>
304 <p>NA</p>
305 </td>
306 </tr>
307 <tr>
308 <td>Chromosome</td>
309 <td>Rv2231c</td>
310 <td>
311 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2231c" target="_blank"
312 rel="noreferrer noopener">GENE_Rv2231c</a>
313 </td>
314 <td>
315 <p>NA</p>
316 </td>
317 <td>True</td>
318 <td>synonymous_variant</td>
319 <td>
320 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2505085..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2505085..None"
321 target="_blank" rel="noreferrer noopener">2505085</a>
322 </td>
323 <td>G</td>
324 <td>A</td>
325 <td>protein_coding</td>
326 <td>c.615C>T</td>
327 <td>p.Ala205Ala</td>
328 <td>LOW</td>
329 <td>
330 <p>NA</p>
331 </td>
332 </tr>
333 <tr>
334 <td>Chromosome</td>
335 <td>Rv2268c</td>
336 <td>
337 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2268c" target="_blank"
338 rel="noreferrer noopener">GENE_Rv2268c</a>
339 </td>
340 <td>
341 <p>NA</p>
342 </td>
343 <td>True</td>
344 <td>synonymous_variant</td>
345 <td>
346 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2543395..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2543395..None"
347 target="_blank" rel="noreferrer noopener">2543395</a>
348 </td>
349 <td>T</td>
350 <td>C</td>
351 <td>protein_coding</td>
352 <td>c.882A>G</td>
353 <td>p.Glu294Glu</td>
354 <td>LOW</td>
355 <td>
356 <p>NA</p>
357 </td>
358 </tr>
359 <tr>
360 <td>Chromosome</td>
361 <td>Rv2357c</td>
362 <td>
363 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2357c" target="_blank"
364 rel="noreferrer noopener">GENE_Rv2357c</a>
365 </td>
366 <td>
367 <p>NA</p>
368 </td>
369 <td>True</td>
370 <td>synonymous_variant</td>
371 <td>
372 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2640807..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2640807..None"
373 target="_blank" rel="noreferrer noopener">2640807</a>
374 </td>
375 <td>G</td>
376 <td>A</td>
377 <td>protein_coding</td>
378 <td>c.258C>T</td>
379 <td>p.Val86Val</td>
380 <td>LOW</td>
381 <td>
382 <p>NA</p>
383 </td>
384 </tr>
385 <tr>
386 <td>Chromosome</td>
387 <td>Rv2472</td>
388 <td>
389 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2472" target="_blank"
390 rel="noreferrer noopener">GENE_Rv2472</a>
391 </td>
392 <td>
393 <p>NA</p>
394 </td>
395 <td>True</td>
396 <td>synonymous_variant</td>
397 <td>
398 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2775361..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2775361..None"
399 target="_blank" rel="noreferrer noopener">2775361</a>
400 </td>
401 <td>C</td>
402 <td>T</td>
403 <td>protein_coding</td>
404 <td>c.90C>T</td>
405 <td>p.Arg30Arg</td>
406 <td>LOW</td>
407 <td>
408 <p>NA</p>
409 </td>
410 </tr>
411 <tr>
412 <td>Chromosome</td>
413 <td>Rv2483c</td>
414 <td>
415 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2483c" target="_blank"
416 rel="noreferrer noopener">GENE_Rv2483c</a>
417 </td>
418 <td>
419 <p>NA</p>
420 </td>
421 <td>True</td>
422 <td>synonymous_variant</td>
423 <td>
424 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2789798..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2789798..None"
425 target="_blank" rel="noreferrer noopener">2789798</a>
426 </td>
427 <td>G</td>
428 <td>T</td>
429 <td>protein_coding</td>
430 <td>c.1225C>A</td>
431 <td>p.Arg409Arg</td>
432 <td>LOW</td>
433 <td>
434 <p>NA</p>
435 </td>
436 </tr>
437 <tr>
438 <td>Chromosome</td>
439 <td>Rv3109</td>
440 <td>
441 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3109" target="_blank"
442 rel="noreferrer noopener">GENE_Rv3109</a>
443 </td>
444 <td>
445 <p>NA</p>
446 </td>
447 <td>True</td>
448 <td>synonymous_variant</td>
449 <td>
450 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3477942..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3477942..None"
451 target="_blank" rel="noreferrer noopener">3477942</a>
452 </td>
453 <td>A</td>
454 <td>G</td>
455 <td>protein_coding</td>
456 <td>c.294A>G</td>
457 <td>p.Thr98Thr</td>
458 <td>LOW</td>
459 <td>
460 <p>NA</p>
461 </td>
462 </tr>
463 <tr>
464 <td>Chromosome</td>
465 <td>Rv3210c</td>
466 <td>
467 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3210c" target="_blank"
468 rel="noreferrer noopener">GENE_Rv3210c</a>
469 </td>
470 <td>
471 <p>NA</p>
472 </td>
473 <td>True</td>
474 <td>synonymous_variant</td>
475 <td>
476 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None"
477 target="_blank" rel="noreferrer noopener">3587446</a>
478 </td>
479 <td>G</td>
480 <td>A</td>
481 <td>protein_coding</td>
482 <td>c.94C>T</td>
483 <td>p.Leu32Leu</td>
484 <td>LOW</td>
485 <td>
486 <p>NA</p>
487 </td>
488 </tr>
489 <tr>
490 <td>Chromosome</td>
491 <td>Rv3799c</td>
492 <td>
493 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
494 rel="noreferrer noopener">GENE_Rv3799c</a>
495 </td>
496 <td>
497 <p>NA</p>
498 </td>
499 <td>True</td>
500 <td>synonymous_variant</td>
501 <td>
502 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None"
503 target="_blank" rel="noreferrer noopener">4254431</a>
504 </td>
505 <td>G</td>
506 <td>A</td>
507 <td>protein_coding</td>
508 <td>c.1518C>T</td>
509 <td>p.Asp506Asp</td>
510 <td>LOW</td>
511 <td>
512 <p>NA</p>
513 </td>
514 </tr>
515 <tr>
516 <td>Chromosome</td>
517 <td>Rv3799c</td>
518 <td>
519 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
520 rel="noreferrer noopener">GENE_Rv3799c</a>
521 </td>
522 <td>
523 <p>NA</p>
524 </td>
525 <td>True</td>
526 <td>missense_variant</td>
527 <td>
528 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None"
529 target="_blank" rel="noreferrer noopener">4254477</a>
530 </td>
531 <td>T</td>
532 <td>C</td>
533 <td>protein_coding</td>
534 <td>c.1472A>G</td>
535 <td>p.His491Arg</td>
536 <td>MODERATE</td>
537 <td>
538 <p>NA</p>
539 </td>
540 </tr>
541 </tbody>
542 <tfoot class="thead-light">
543 <tr>
544 <th scope="col">CHR</th>
545 <th scope="col">GENE</th>
546 <th scope="col">LOCUS</th>
547 <th scope="col">PRODUCT</th>
548 <th scope="col">TYPE</th>
549 <th scope="col">EFFECT</th>
550 <th scope="col">POS</th>
551 <th scope="col">REF</th>
552 <th scope="col">ALT</th>
553 <th scope="col">BIOTYPE</th>
554 <th scope="col">NUCLEOTIDE</th>
555 <th scope="col">CONSEQUENCE</th>
556 <th scope="col">IMPACT</th>
557 <th scope="col">PATHWAY</th>
558 </tr>
559 </tfoot>
560 </table>
561 </div>
562 </main>
563 <div class="mt-5">
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