Mercurial > repos > iuc > tbvcfreport

comparison test-data/vcf_with_no_protein_report.html @ 2:bda58fe79026 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
author iuc
date Thu, 17 Mar 2022 07:32:28 +0000
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1 <!DOCTYPE html>
2 <html>
3
4 <head>
5 <title></title>
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16
17 <body>
18 <div class="container">
19 <div class="row">
20 <h2 class="mt-5">
21 vcf_with_no_protein Report
22 </h2>
23 </div>
24 <hr>
25 <div class="row justify-content-center align-items-center">
26 <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
27 <thead class="thead-light">
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">TYPE</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>Rv3753c</td>
50 <td>
51 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3753c" target="_blank"
52 rel="noreferrer noopener">Rv3753c</a>
53 </td>
54 <td>
55 <a href="https://explorer.sanbi.ac.za/search?q=O69720"
56 target="_blank" rel="noreferrer noopener">O69720</a>
57 </td>
58 <td>snp</td>
59 <td>missense_variant</td>
60 <td>
61 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..4200220&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..4200220"
62 target="_blank" rel="noreferrer noopener">4200220</a>
63 </td>
64 <td>G</td>
65 <td>A</td>
66 <td>protein_coding</td>
67 <td>c.2C>T</td>
68 <td>p.Thr1Met</td>
69 <td>MODERATE</td>
70 <td>
71 <p>NA</p>
72 </td>
73 </tr>
74 <tr>
75 <td>Chromosome</td>
76 <td>Rv3756c</td>
77 <td>
78 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3756c" target="_blank"
79 rel="noreferrer noopener">Rv3756c</a>
80 </td>
81 <td>
82 <a href="https://explorer.sanbi.ac.za/search?q=O69722"
83 target="_blank" rel="noreferrer noopener">O69722</a>
84 </td>
85 <td>snp</td>
86 <td>synonymous_variant</td>
87 <td>
88 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..4202383&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..4202383"
89 target="_blank" rel="noreferrer noopener">4202383</a>
90 </td>
91 <td>C</td>
92 <td>A</td>
93 <td>protein_coding</td>
94 <td>c.231G>T</td>
95 <td>p.Val77Val</td>
96 <td>LOW</td>
97 <td>
98 <p>
99 <small>
100 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu02010" target="_blank"
101 rel="noreferrer noopener">ABC transporters</a>
102 </small>
103 </p>
104 </td>
105 </tr>
106 <tr>
107 <td>Chromosome</td>
108 <td>Rv3759c</td>
109 <td>
110 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3759c" target="_blank"
111 rel="noreferrer noopener">Rv3759c</a>
112 </td>
113 <td>
114 <a href="https://explorer.sanbi.ac.za/search?q=O69725"
115 target="_blank" rel="noreferrer noopener">O69725</a>
116 </td>
117 <td>snp</td>
118 <td>missense_variant</td>
119 <td>
120 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..4205120&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..4205120"
121 target="_blank" rel="noreferrer noopener">4205120</a>
122 </td>
123 <td>G</td>
124 <td>A</td>
125 <td>protein_coding</td>
126 <td>c.254C>T</td>
127 <td>p.Pro85Leu</td>
128 <td>MODERATE</td>
129 <td>
130 <p>
131 <small>
132 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu02010" target="_blank"
133 rel="noreferrer noopener">ABC transporters</a>
134 </small>
135 </p>
136 </td>
137 </tr>
138 <tr>
139 <td>Chromosome</td>
140 <td>Rv3764c</td>
141 <td>
142 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3764c" target="_blank"
143 rel="noreferrer noopener">Rv3764c</a>
144 </td>
145 <td>
146 <a href="https://explorer.sanbi.ac.za/search?q=O69729"
147 target="_blank" rel="noreferrer noopener">O69729</a>
148 </td>
149 <td>snp</td>
150 <td>missense_variant</td>
151 <td>
152 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..4210876&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..4210876"
153 target="_blank" rel="noreferrer noopener">4210876</a>
154 </td>
155 <td>C</td>
156 <td>T</td>
157 <td>protein_coding</td>
158 <td>c.134G>A</td>
159 <td>p.Arg45His</td>
160 <td>MODERATE</td>
161 <td>
162 <p>NA</p>
163 </td>
164 </tr>
165 <tr>
166 <td>Chromosome</td>
167 <td>Rv3769</td>
168 <td>
169 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3769" target="_blank"
170 rel="noreferrer noopener">Rv3769</a>
171 </td>
172 <td>
173 <a href="https://explorer.sanbi.ac.za/search?q=P72036"
174 target="_blank" rel="noreferrer noopener">P72036</a>
175 </td>
176 <td>snp</td>
177 <td>missense_variant</td>
178 <td>
179 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4214747..4214747&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4214747..4214747"
180 target="_blank" rel="noreferrer noopener">4214747</a>
181 </td>
182 <td>C</td>
183 <td>T</td>
184 <td>protein_coding</td>
185 <td>c.133C>T</td>
186 <td>p.His45Tyr</td>
187 <td>MODERATE</td>
188 <td>
189 <p>NA</p>
190 </td>
191 </tr>
192 <tr>
193 <td>Chromosome</td>
194 <td>Rv3770c</td>
195 <td>
196 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3770c" target="_blank"
197 rel="noreferrer noopener">Rv3770c</a>
198 </td>
199 <td>
200 <a href="https://explorer.sanbi.ac.za/search?q=P72037"
201 target="_blank" rel="noreferrer noopener">P72037</a>
202 </td>
203 <td>snp</td>
204 <td>missense_variant</td>
205 <td>
206 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4215484..4215484&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4215484..4215484"
207 target="_blank" rel="noreferrer noopener">4215484</a>
208 </td>
209 <td>C</td>
210 <td>G</td>
211 <td>protein_coding</td>
212 <td>c.292G>C</td>
213 <td>p.Ala98Pro</td>
214 <td>MODERATE</td>
215 <td>
216 <p>NA</p>
217 </td>
218 </tr>
219 <tr>
220 <td>Chromosome</td>
221 <td>Rv3772</td>
222 <td>
223 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3772" target="_blank"
224 rel="noreferrer noopener">Rv3772</a>
225 </td>
226 <td>
227 <a href="https://explorer.sanbi.ac.za/search?q=P9WML5"
228 target="_blank" rel="noreferrer noopener">P9WML5</a>
229 </td>
230 <td>snp</td>
231 <td>missense_variant</td>
232 <td>
233 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4217557..4217557&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4217557..4217557"
234 target="_blank" rel="noreferrer noopener">4217557</a>
235 </td>
236 <td>G</td>
237 <td>A</td>
238 <td>protein_coding</td>
239 <td>c.424G>A</td>
240 <td>p.Ala142Thr</td>
241 <td>MODERATE</td>
242 <td>
243 <p>
244 <small>
245 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00400" target="_blank"
246 rel="noreferrer noopener">Phenylalanine, tyrosine and tryptophan biosynthesis</a>
247 </small>
248 </p>
249 <p>
250 <small>
251 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00360" target="_blank"
252 rel="noreferrer noopener">Phenylalanine metabolism</a>
253 </small>
254 </p>
255 <p>
256 <small>
257 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00340" target="_blank"
258 rel="noreferrer noopener">Histidine metabolism</a>
259 </small>
260 </p>
261 <p>
262 <small>
263 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00350" target="_blank"
264 rel="noreferrer noopener">Tyrosine metabolism</a>
265 </small>
266 </p>
267 </td>
268 </tr>
269 <tr>
270 <td>Chromosome</td>
271 <td>Rv3777</td>
272 <td>
273 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3777" target="_blank"
274 rel="noreferrer noopener">Rv3777</a>
275 </td>
276 <td>
277 <a href="https://explorer.sanbi.ac.za/search?q=P72043"
278 target="_blank" rel="noreferrer noopener">P72043</a>
279 </td>
280 <td>snp</td>
281 <td>missense_variant</td>
282 <td>
283 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4223172..4223172&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4223172..4223172"
284 target="_blank" rel="noreferrer noopener">4223172</a>
285 </td>
286 <td>C</td>
287 <td>T</td>
288 <td>protein_coding</td>
289 <td>c.479C>T</td>
290 <td>p.Ala160Val</td>
291 <td>MODERATE</td>
292 <td>
293 <p>NA</p>
294 </td>
295 </tr>
296 <tr>
297 <td>Chromosome</td>
298 <td>Rv3785</td>
299 <td>
300 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3785" target="_blank"
301 rel="noreferrer noopener">Rv3785</a>
302 </td>
303 <td>
304 <a href="https://explorer.sanbi.ac.za/search?q=P9WKX1"
305 target="_blank" rel="noreferrer noopener">P9WKX1</a>
306 </td>
307 <td>snp</td>
308 <td>synonymous_variant</td>
309 <td>
310 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4232327..4232327&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4232327..4232327"
311 target="_blank" rel="noreferrer noopener">4232327</a>
312 </td>
313 <td>G</td>
314 <td>A</td>
315 <td>protein_coding</td>
316 <td>c.1008G>A</td>
317 <td>p.Arg336Arg</td>
318 <td>LOW</td>
319 <td>
320 <p>NA</p>
321 </td>
322 </tr>
323 <tr>
324 <td>Chromosome</td>
325 <td>Rv3792</td>
326 <td>
327 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3792" target="_blank"
328 rel="noreferrer noopener">Rv3792</a>
329 </td>
330 <td>
331 <a href="https://explorer.sanbi.ac.za/search?q=P9WN03"
332 target="_blank" rel="noreferrer noopener">P9WN03</a>
333 </td>
334 <td>snp</td>
335 <td>synonymous_variant</td>
336 <td>
337 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4238963..4238963&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4238963..4238963"
338 target="_blank" rel="noreferrer noopener">4238963</a>
339 </td>
340 <td>C</td>
341 <td>T</td>
342 <td>protein_coding</td>
343 <td>c.1032C>T</td>
344 <td>p.His344His</td>
345 <td>LOW</td>
346 <td>
347 <p>
348 <small>
349 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank"
350 rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a>
351 </small>
352 </p>
353 </td>
354 </tr>
355 <tr>
356 <td>Chromosome</td>
357 <td>Rv3792</td>
358 <td>
359 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3792" target="_blank"
360 rel="noreferrer noopener">Rv3792</a>
361 </td>
362 <td>
363 <a href="https://explorer.sanbi.ac.za/search?q=P9WN03"
364 target="_blank" rel="noreferrer noopener">P9WN03</a>
365 </td>
366 <td>snp</td>
367 <td>missense_variant</td>
368 <td>
369 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4239274..4239274&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4239274..4239274"
370 target="_blank" rel="noreferrer noopener">4239274</a>
371 </td>
372 <td>C</td>
373 <td>G</td>
374 <td>protein_coding</td>
375 <td>c.1343C>G</td>
376 <td>p.Pro448Arg</td>
377 <td>MODERATE</td>
378 <td>
379 <p>
380 <small>
381 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank"
382 rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a>
383 </small>
384 </p>
385 </td>
386 </tr>
387 <tr>
388 <td>Chromosome</td>
389 <td>Rv3793</td>
390 <td>
391 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3793" target="_blank"
392 rel="noreferrer noopener">Rv3793</a>
393 </td>
394 <td>
395 <a href="https://explorer.sanbi.ac.za/search?q=P9WNL5"
396 target="_blank" rel="noreferrer noopener">P9WNL5</a>
397 </td>
398 <td>snp</td>
399 <td>missense_variant</td>
400 <td>
401 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4240671..4240671&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4240671..4240671"
402 target="_blank" rel="noreferrer noopener">4240671</a>
403 </td>
404 <td>T</td>
405 <td>C</td>
406 <td>protein_coding</td>
407 <td>c.809T>C</td>
408 <td>p.Ile270Thr</td>
409 <td>MODERATE</td>
410 <td>
411 <p>
412 <small>
413 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00571" target="_blank"
414 rel="noreferrer noopener">Lipoarabinomannan (LAM) biosynthesis</a>
415 </small>
416 </p>
417 </td>
418 </tr>
419 <tr>
420 <td>Chromosome</td>
421 <td>Rv3795</td>
422 <td>
423 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3795" target="_blank"
424 rel="noreferrer noopener">Rv3795</a>
425 </td>
426 <td>
427 <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7"
428 target="_blank" rel="noreferrer noopener">P9WNL7</a>
429 </td>
430 <td>snp</td>
431 <td>missense_variant</td>
432 <td>
433 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247429..4247429&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247429..4247429"
434 target="_blank" rel="noreferrer noopener">4247429</a>
435 </td>
436 <td>A</td>
437 <td>G</td>
438 <td>protein_coding</td>
439 <td>c.916A>G</td>
440 <td>p.Met306Val</td>
441 <td>MODERATE</td>
442 <td>
443 <p>
444 <small>
445 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank"
446 rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a>
447 </small>
448 </p>
449 </td>
450 </tr>
451 <tr>
452 <td>Chromosome</td>
453 <td>Rv3795</td>
454 <td>
455 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3795" target="_blank"
456 rel="noreferrer noopener">Rv3795</a>
457 </td>
458 <td>
459 <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7"
460 target="_blank" rel="noreferrer noopener">P9WNL7</a>
461 </td>
462 <td>snp</td>
463 <td>missense_variant</td>
464 <td>
465 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..4247646&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..4247646"
466 target="_blank" rel="noreferrer noopener">4247646</a>
467 </td>
468 <td>C</td>
469 <td>A</td>
470 <td>protein_coding</td>
471 <td>c.1133C>A</td>
472 <td>p.Ala378Glu</td>
473 <td>MODERATE</td>
474 <td>
475 <p>
476 <small>
477 <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank"
478 rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a>
479 </small>
480 </p>
481 </td>
482 </tr>
483 <tr>
484 <td>Chromosome</td>
485 <td>Rv3797</td>
486 <td>
487 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3797" target="_blank"
488 rel="noreferrer noopener">Rv3797</a>
489 </td>
490 <td>
491 <a href="https://explorer.sanbi.ac.za/search?q=O53577"
492 target="_blank" rel="noreferrer noopener">O53577</a>
493 </td>
494 <td>snp</td>
495 <td>synonymous_variant</td>
496 <td>
497 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..4251297&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..4251297"
498 target="_blank" rel="noreferrer noopener">4251297</a>
499 </td>
500 <td>C</td>
501 <td>G</td>
502 <td>protein_coding</td>
503 <td>c.213C>G</td>
504 <td>p.Gly71Gly</td>
505 <td>LOW</td>
506 <td>
507 <p>NA</p>
508 </td>
509 </tr>
510 <tr>
511 <td>Chromosome</td>
512 <td>Rv3798</td>
513 <td>
514 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3798" target="_blank"
515 rel="noreferrer noopener">Rv3798</a>
516 </td>
517 <td>
518 <p>NA</p>
519 </td>
520 <td>snp</td>
521 <td>missense_variant</td>
522 <td>
523 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254290..4254290&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..4254290"
524 target="_blank" rel="noreferrer noopener">4254290</a>
525 </td>
526 <td>T</td>
527 <td>G</td>
528 <td>protein_coding</td>
529 <td>c.1298T>G</td>
530 <td>p.Leu433Arg</td>
531 <td>MODERATE</td>
532 <td>
533 <p>NA</p>
534 </td>
535 </tr>
536 <tr>
537 <td>Chromosome</td>
538 <td>Rv3799c</td>
539 <td>
540 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3799c" target="_blank"
541 rel="noreferrer noopener">Rv3799c</a>
542 </td>
543 <td>
544 <a href="https://explorer.sanbi.ac.za/search?q=O53578"
545 target="_blank" rel="noreferrer noopener">O53578</a>
546 </td>
547 <td>snp</td>
548 <td>missense_variant</td>
549 <td>
550 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..4254478&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..4254478"
551 target="_blank" rel="noreferrer noopener">4254478</a>
552 </td>
553 <td>G</td>
554 <td>A</td>
555 <td>protein_coding</td>
556 <td>c.1471C>T</td>
557 <td>p.His491Tyr</td>
558 <td>MODERATE</td>
559 <td>
560 <p>NA</p>
561 </td>
562 </tr>
563 <tr>
564 <td>Chromosome</td>
565 <td>Rv3801c</td>
566 <td>
567 <a href="https://explorer.sanbi.ac.za/gene?q=Rv3801c" target="_blank"
568 rel="noreferrer noopener">Rv3801c</a>
569 </td>
570 <td>
571 <a href="https://explorer.sanbi.ac.za/search?q=O53580"
572 target="_blank" rel="noreferrer noopener">O53580</a>
573 </td>
574 <td>snp</td>
575 <td>missense_variant</td>
576 <td>
577 <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..4261499&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..4261499"
578 target="_blank" rel="noreferrer noopener">4261499</a>
579 </td>
580 <td>A</td>
581 <td>G</td>
582 <td>protein_coding</td>
583 <td>c.1568T>C</td>
584 <td>p.Val523Ala</td>
585 <td>MODERATE</td>
586 <td>
587 <p>NA</p>
588 </td>
589 </tr>
590 </tbody>
591 <tfoot class="thead-light">
592 <tr>
593 <th scope="col">CHR</th>
594 <th scope="col">GENE</th>
595 <th scope="col">LOCUS</th>
596 <th scope="col">PRODUCT</th>
597 <th scope="col">TYPE</th>
598 <th scope="col">EFFECT</th>
599 <th scope="col">POS</th>
600 <th scope="col">REF</th>
601 <th scope="col">ALT</th>
602 <th scope="col">BIOTYPE</th>
603 <th scope="col">NUCLEOTIDE</th>
604 <th scope="col">CONSEQUENCE</th>
605 <th scope="col">IMPACT</th>
606 <th scope="col">PATHWAY</th>
607 </tr>
608 </tfoot>
609 </table>
610 </div>
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