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comparison test-data/rif_resistant_variants_report_with_lineage.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
19 <div class="row"> 19 <div class="row">
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 <div class="row">
25 <table class="table table-striped table-hover table-responsive-md">
26 <caption>Lineage Info</caption>
27 <thead class="thead-light">
28 <tr>
29 <th scope="col">Lineage</th>
30 <th scope="col">Lineage support fraction</th>
31 <th scope="col">Family</th>
32 <th scope="col">RD</th>
33 </tr>
34 </thead>
35 <tbody>
36 <tr>
37 <td>lineage2</td>
38 <td>0.9940119760479041</td>
39 <td>East-Asian</td>
40 <td>RD105</td>
41 </tr>
42 <tr>
43 <td>lineage2.2.2</td>
44 <td>1.0</td>
45 <td>East-Asian (Beijing)</td>
46 <td>RD105;RD207</td>
47 </tr>
48 </tbody>
49 </table>
50 </div>
24 <hr> 51 <hr>
25 <div class="row justify-content-center align-items-center"> 52 <div class="row justify-content-center align-items-center">
26 <table id="lineagereport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0"> 53 <table id="lineagereport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
27 <thead class="thead-light"> 54 <thead class="thead-light">
28 <tr> 55 <tr>
33 <th scope="col">Agreement</th> 60 <th scope="col">Agreement</th>
34 </tr> 61 </tr>
35 </thead> 62 </thead>
36 <tbody> 63 <tbody>
37 <tr> 64 <tr>
38 <td>lineage2</td> 65 <td></td>
39 <td>East-Asian</td> 66 <td></td>
40 <td>Beijing</td> 67 <td></td>
41 <td>RD105</td> 68 <td></td>
42 <td>1.0</td> 69 <td></td>
43 </tr> 70 </tr>
44 <tr> 71 <tr>
45 <td>lineage2.2</td> 72 <td></td>
46 <td>East-Asian (Beijing)</td> 73 <td></td>
47 <td>Beijing-RD207</td> 74 <td></td>
48 <td>RD105;RD207</td> 75 <td></td>
49 <td>1.0</td> 76 <td></td>
50 </tr>
51 <tr>
52 <td>lineage2.2.2</td>
53 <td>East-Asian (Beijing)</td>
54 <td>Beijing-RD105/RD207</td>
55 <td>RD105;RD207</td>
56 <td>1.0</td>
57 </tr> 77 </tr>
58 </tbody> 78 </tbody>
59 </table> 79 </table>
60 </div> 80 </div>
61 <div> 81 <div class="row justify-content-center align-items-center">
62 <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html" 82 <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
63 target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p> 83 <thead class="thead-light">
64 <p>Kindly check if the '<strong>ANN</strong>' field is present.</p> 84 <tr>
85 <th scope="col">CHR</th>
86 <th scope="col">GENE</th>
87 <th scope="col">LOCUS</th>
88 <th scope="col">PRODUCT</th>
89 <th scope="col">IS_SNV</th>
90 <th scope="col">EFFECT</th>
91 <th scope="col">POS</th>
92 <th scope="col">REF</th>
93 <th scope="col">ALT</th>
94 <th scope="col">BIOTYPE</th>
95 <th scope="col">NUCLEOTIDE</th>
96 <th scope="col">CONSEQUENCE</th>
97 <th scope="col">IMPACT</th>
98 <th scope="col">PATHWAY</th>
99 </tr>
100 </thead>
101 <tbody>
102
103 <tr>
104 <td>Chromosome</td>
105 <td>Rv0014c</td>
106 <td>
107 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0014c" target="_blank"
108 rel="noreferrer noopener">GENE_Rv0014c</a>
109 </td>
110 <td>
111 <p>NA</p>
112 </td>
113 <td>True</td>
114 <td>synonymous_variant</td>
115 <td>
116 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A15890..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A15890..None"
117 target="_blank" rel="noreferrer noopener">15890</a>
118 </td>
119 <td>G</td>
120 <td>A</td>
121 <td>protein_coding</td>
122 <td>c.1581C>T</td>
123 <td>p.Ser527Ser</td>
124 <td>LOW</td>
125 <td>
126 <p>NA</p>
127 </td>
128 </tr>
129 <tr>
130 <td>Chromosome</td>
131 <td>Rv0127</td>
132 <td>
133 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0127" target="_blank"
134 rel="noreferrer noopener">GENE_Rv0127</a>
135 </td>
136 <td>
137 <p>NA</p>
138 </td>
139 <td>True</td>
140 <td>synonymous_variant</td>
141 <td>
142 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A154990..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A154990..None"
143 target="_blank" rel="noreferrer noopener">154990</a>
144 </td>
145 <td>G</td>
146 <td>T</td>
147 <td>protein_coding</td>
148 <td>c.759G>T</td>
149 <td>p.Arg253Arg</td>
150 <td>LOW</td>
151 <td>
152 <p>NA</p>
153 </td>
154 </tr>
155 <tr>
156 <td>Chromosome</td>
157 <td>Rv0284</td>
158 <td>
159 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0284" target="_blank"
160 rel="noreferrer noopener">GENE_Rv0284</a>
161 </td>
162 <td>
163 <p>NA</p>
164 </td>
165 <td>True</td>
166 <td>synonymous_variant</td>
167 <td>
168 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A346693..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A346693..None"
169 target="_blank" rel="noreferrer noopener">346693</a>
170 </td>
171 <td>G</td>
172 <td>T</td>
173 <td>protein_coding</td>
174 <td>c.1059G>T</td>
175 <td>p.Ser353Ser</td>
176 <td>LOW</td>
177 <td>
178 <p>NA</p>
179 </td>
180 </tr>
181 <tr>
182 <td>Chromosome</td>
183 <td>Rv0372c</td>
184 <td>
185 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0372c" target="_blank"
186 rel="noreferrer noopener">GENE_Rv0372c</a>
187 </td>
188 <td>
189 <p>NA</p>
190 </td>
191 <td>True</td>
192 <td>synonymous_variant</td>
193 <td>
194 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A449194..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A449194..None"
195 target="_blank" rel="noreferrer noopener">449194</a>
196 </td>
197 <td>G</td>
198 <td>A</td>
199 <td>protein_coding</td>
200 <td>c.192C>T</td>
201 <td>p.Gly64Gly</td>
202 <td>LOW</td>
203 <td>
204 <p>NA</p>
205 </td>
206 </tr>
207 <tr>
208 <td>Chromosome</td>
209 <td>Rv0411c</td>
210 <td>
211 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0411c" target="_blank"
212 rel="noreferrer noopener">GENE_Rv0411c</a>
213 </td>
214 <td>
215 <p>NA</p>
216 </td>
217 <td>True</td>
218 <td>synonymous_variant</td>
219 <td>
220 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A497491..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A497491..None"
221 target="_blank" rel="noreferrer noopener">497491</a>
222 </td>
223 <td>G</td>
224 <td>A</td>
225 <td>protein_coding</td>
226 <td>c.810C>T</td>
227 <td>p.Asp270Asp</td>
228 <td>LOW</td>
229 <td>
230 <p>NA</p>
231 </td>
232 </tr>
233 <tr>
234 <td>Chromosome</td>
235 <td>Rv0667</td>
236 <td>
237 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0667" target="_blank"
238 rel="noreferrer noopener">GENE_Rv0667</a>
239 </td>
240 <td>
241 <p>NA</p>
242 </td>
243 <td>True</td>
244 <td>missense_variant</td>
245 <td>
246 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A761110..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A761110..None"
247 target="_blank" rel="noreferrer noopener">761110</a>
248 </td>
249 <td>A</td>
250 <td>T</td>
251 <td>protein_coding</td>
252 <td>c.1304A>T</td>
253 <td>p.Asp435Val</td>
254 <td>MODERATE</td>
255 <td>
256 <p>NA</p>
257 </td>
258 </tr>
259 <tr>
260 <td>Chromosome</td>
261 <td>Rv0715</td>
262 <td>
263 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0715" target="_blank"
264 rel="noreferrer noopener">GENE_Rv0715</a>
265 </td>
266 <td>
267 <p>NA</p>
268 </td>
269 <td>True</td>
270 <td>synonymous_variant</td>
271 <td>
272 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A811753..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A811753..None"
273 target="_blank" rel="noreferrer noopener">811753</a>
274 </td>
275 <td>C</td>
276 <td>T</td>
277 <td>protein_coding</td>
278 <td>c.12C>T</td>
279 <td>p.His4His</td>
280 <td>LOW</td>
281 <td>
282 <p>NA</p>
283 </td>
284 </tr>
285 <tr>
286 <td>Chromosome</td>
287 <td>Rv1391</td>
288 <td>
289 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1391" target="_blank"
290 rel="noreferrer noopener">GENE_Rv1391</a>
291 </td>
292 <td>
293 <p>NA</p>
294 </td>
295 <td>True</td>
296 <td>synonymous_variant</td>
297 <td>
298 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1565566..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1565566..None"
299 target="_blank" rel="noreferrer noopener">1565566</a>
300 </td>
301 <td>C</td>
302 <td>T</td>
303 <td>protein_coding</td>
304 <td>c.126C>T</td>
305 <td>p.Pro42Pro</td>
306 <td>LOW</td>
307 <td>
308 <p>NA</p>
309 </td>
310 </tr>
311 <tr>
312 <td>Chromosome</td>
313 <td>Rv1630</td>
314 <td>
315 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1630" target="_blank"
316 rel="noreferrer noopener">GENE_Rv1630</a>
317 </td>
318 <td>
319 <p>NA</p>
320 </td>
321 <td>True</td>
322 <td>synonymous_variant</td>
323 <td>
324 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1834177..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1834177..None"
325 target="_blank" rel="noreferrer noopener">1834177</a>
326 </td>
327 <td>A</td>
328 <td>C</td>
329 <td>protein_coding</td>
330 <td>c.636A>C</td>
331 <td>p.Arg212Arg</td>
332 <td>LOW</td>
333 <td>
334 <p>NA</p>
335 </td>
336 </tr>
337 <tr>
338 <td>Chromosome</td>
339 <td>Rv1640c</td>
340 <td>
341 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1640c" target="_blank"
342 rel="noreferrer noopener">GENE_Rv1640c</a>
343 </td>
344 <td>
345 <p>NA</p>
346 </td>
347 <td>True</td>
348 <td>synonymous_variant</td>
349 <td>
350 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1849051..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1849051..None"
351 target="_blank" rel="noreferrer noopener">1849051</a>
352 </td>
353 <td>C</td>
354 <td>T</td>
355 <td>protein_coding</td>
356 <td>c.2985G>A</td>
357 <td>p.Pro995Pro</td>
358 <td>LOW</td>
359 <td>
360 <p>NA</p>
361 </td>
362 </tr>
363 <tr>
364 <td>Chromosome</td>
365 <td>Rv2231c</td>
366 <td>
367 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2231c" target="_blank"
368 rel="noreferrer noopener">GENE_Rv2231c</a>
369 </td>
370 <td>
371 <p>NA</p>
372 </td>
373 <td>True</td>
374 <td>synonymous_variant</td>
375 <td>
376 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2505085..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2505085..None"
377 target="_blank" rel="noreferrer noopener">2505085</a>
378 </td>
379 <td>G</td>
380 <td>A</td>
381 <td>protein_coding</td>
382 <td>c.615C>T</td>
383 <td>p.Ala205Ala</td>
384 <td>LOW</td>
385 <td>
386 <p>NA</p>
387 </td>
388 </tr>
389 <tr>
390 <td>Chromosome</td>
391 <td>Rv2268c</td>
392 <td>
393 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2268c" target="_blank"
394 rel="noreferrer noopener">GENE_Rv2268c</a>
395 </td>
396 <td>
397 <p>NA</p>
398 </td>
399 <td>True</td>
400 <td>synonymous_variant</td>
401 <td>
402 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2543395..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2543395..None"
403 target="_blank" rel="noreferrer noopener">2543395</a>
404 </td>
405 <td>T</td>
406 <td>C</td>
407 <td>protein_coding</td>
408 <td>c.882A>G</td>
409 <td>p.Glu294Glu</td>
410 <td>LOW</td>
411 <td>
412 <p>NA</p>
413 </td>
414 </tr>
415 <tr>
416 <td>Chromosome</td>
417 <td>Rv2357c</td>
418 <td>
419 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2357c" target="_blank"
420 rel="noreferrer noopener">GENE_Rv2357c</a>
421 </td>
422 <td>
423 <p>NA</p>
424 </td>
425 <td>True</td>
426 <td>synonymous_variant</td>
427 <td>
428 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2640807..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2640807..None"
429 target="_blank" rel="noreferrer noopener">2640807</a>
430 </td>
431 <td>G</td>
432 <td>A</td>
433 <td>protein_coding</td>
434 <td>c.258C>T</td>
435 <td>p.Val86Val</td>
436 <td>LOW</td>
437 <td>
438 <p>NA</p>
439 </td>
440 </tr>
441 <tr>
442 <td>Chromosome</td>
443 <td>Rv2472</td>
444 <td>
445 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2472" target="_blank"
446 rel="noreferrer noopener">GENE_Rv2472</a>
447 </td>
448 <td>
449 <p>NA</p>
450 </td>
451 <td>True</td>
452 <td>synonymous_variant</td>
453 <td>
454 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2775361..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2775361..None"
455 target="_blank" rel="noreferrer noopener">2775361</a>
456 </td>
457 <td>C</td>
458 <td>T</td>
459 <td>protein_coding</td>
460 <td>c.90C>T</td>
461 <td>p.Arg30Arg</td>
462 <td>LOW</td>
463 <td>
464 <p>NA</p>
465 </td>
466 </tr>
467 <tr>
468 <td>Chromosome</td>
469 <td>Rv2483c</td>
470 <td>
471 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2483c" target="_blank"
472 rel="noreferrer noopener">GENE_Rv2483c</a>
473 </td>
474 <td>
475 <p>NA</p>
476 </td>
477 <td>True</td>
478 <td>synonymous_variant</td>
479 <td>
480 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2789798..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2789798..None"
481 target="_blank" rel="noreferrer noopener">2789798</a>
482 </td>
483 <td>G</td>
484 <td>T</td>
485 <td>protein_coding</td>
486 <td>c.1225C>A</td>
487 <td>p.Arg409Arg</td>
488 <td>LOW</td>
489 <td>
490 <p>NA</p>
491 </td>
492 </tr>
493 <tr>
494 <td>Chromosome</td>
495 <td>Rv3109</td>
496 <td>
497 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3109" target="_blank"
498 rel="noreferrer noopener">GENE_Rv3109</a>
499 </td>
500 <td>
501 <p>NA</p>
502 </td>
503 <td>True</td>
504 <td>synonymous_variant</td>
505 <td>
506 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3477942..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3477942..None"
507 target="_blank" rel="noreferrer noopener">3477942</a>
508 </td>
509 <td>A</td>
510 <td>G</td>
511 <td>protein_coding</td>
512 <td>c.294A>G</td>
513 <td>p.Thr98Thr</td>
514 <td>LOW</td>
515 <td>
516 <p>NA</p>
517 </td>
518 </tr>
519 <tr>
520 <td>Chromosome</td>
521 <td>Rv3210c</td>
522 <td>
523 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3210c" target="_blank"
524 rel="noreferrer noopener">GENE_Rv3210c</a>
525 </td>
526 <td>
527 <p>NA</p>
528 </td>
529 <td>True</td>
530 <td>synonymous_variant</td>
531 <td>
532 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None"
533 target="_blank" rel="noreferrer noopener">3587446</a>
534 </td>
535 <td>G</td>
536 <td>A</td>
537 <td>protein_coding</td>
538 <td>c.94C>T</td>
539 <td>p.Leu32Leu</td>
540 <td>LOW</td>
541 <td>
542 <p>NA</p>
543 </td>
544 </tr>
545 <tr>
546 <td>Chromosome</td>
547 <td>Rv3799c</td>
548 <td>
549 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
550 rel="noreferrer noopener">GENE_Rv3799c</a>
551 </td>
552 <td>
553 <p>NA</p>
554 </td>
555 <td>True</td>
556 <td>synonymous_variant</td>
557 <td>
558 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None"
559 target="_blank" rel="noreferrer noopener">4254431</a>
560 </td>
561 <td>G</td>
562 <td>A</td>
563 <td>protein_coding</td>
564 <td>c.1518C>T</td>
565 <td>p.Asp506Asp</td>
566 <td>LOW</td>
567 <td>
568 <p>NA</p>
569 </td>
570 </tr>
571 <tr>
572 <td>Chromosome</td>
573 <td>Rv3799c</td>
574 <td>
575 <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
576 rel="noreferrer noopener">GENE_Rv3799c</a>
577 </td>
578 <td>
579 <p>NA</p>
580 </td>
581 <td>True</td>
582 <td>missense_variant</td>
583 <td>
584 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None"
585 target="_blank" rel="noreferrer noopener">4254477</a>
586 </td>
587 <td>T</td>
588 <td>C</td>
589 <td>protein_coding</td>
590 <td>c.1472A>G</td>
591 <td>p.His491Arg</td>
592 <td>MODERATE</td>
593 <td>
594 <p>NA</p>
595 </td>
596 </tr>
597 </tbody>
598 <tfoot class="thead-light">
599 <tr>
600 <th scope="col">CHR</th>
601 <th scope="col">GENE</th>
602 <th scope="col">LOCUS</th>
603 <th scope="col">PRODUCT</th>
604 <th scope="col">TYPE</th>
605 <th scope="col">EFFECT</th>
606 <th scope="col">POS</th>
607 <th scope="col">REF</th>
608 <th scope="col">ALT</th>
609 <th scope="col">BIOTYPE</th>
610 <th scope="col">NUCLEOTIDE</th>
611 <th scope="col">CONSEQUENCE</th>
612 <th scope="col">IMPACT</th>
613 <th scope="col">PATHWAY</th>
614 </tr>
615 </tfoot>
616 </table>
617 </div>
618 </main>
619 <div class="mt-5">
65 </div> 620 </div>
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