Mercurial > repos > iuc > tbvcfreport
diff test-data/rif_resistant_variants_report_with_lineage.html @ 3:42818629ec4c draft
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 |
| children |
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--- a/test-data/rif_resistant_variants_report_with_lineage.html Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_variants_report_with_lineage.html Fri May 31 20:06:49 2024 +0000 @@ -21,6 +21,33 @@ rif_resistant Report </h2> </div> + <div class="row"> + <table class="table table-striped table-hover table-responsive-md"> + <caption>Lineage Info</caption> + <thead class="thead-light"> + <tr> + <th scope="col">Lineage</th> + <th scope="col">Lineage support fraction</th> + <th scope="col">Family</th> + <th scope="col">RD</th> + </tr> + </thead> + <tbody> + <tr> + <td>lineage2</td> + <td>0.9940119760479041</td> + <td>East-Asian</td> + <td>RD105</td> + </tr> + <tr> + <td>lineage2.2.2</td> + <td>1.0</td> + <td>East-Asian (Beijing)</td> + <td>RD105;RD207</td> + </tr> + </tbody> + </table> + </div> <hr> <div class="row justify-content-center align-items-center"> <table id="lineagereport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0"> @@ -35,33 +62,561 @@ </thead> <tbody> <tr> - <td>lineage2</td> - <td>East-Asian</td> - <td>Beijing</td> - <td>RD105</td> - <td>1.0</td> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> </tr> <tr> - <td>lineage2.2</td> - <td>East-Asian (Beijing)</td> - <td>Beijing-RD207</td> - <td>RD105;RD207</td> - <td>1.0</td> - </tr> - <tr> - <td>lineage2.2.2</td> - <td>East-Asian (Beijing)</td> - <td>Beijing-RD105/RD207</td> - <td>RD105;RD207</td> - <td>1.0</td> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> </tr> </tbody> </table> </div> -<div> - <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html" - target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p> - <p>Kindly check if the '<strong>ANN</strong>' field is present.</p> +<div class="row justify-content-center align-items-center"> + <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0"> + <thead class="thead-light"> + <tr> + <th scope="col">CHR</th> + <th scope="col">GENE</th> + <th scope="col">LOCUS</th> + <th scope="col">PRODUCT</th> + <th scope="col">IS_SNV</th> + <th scope="col">EFFECT</th> + <th scope="col">POS</th> + <th scope="col">REF</th> + <th scope="col">ALT</th> + <th scope="col">BIOTYPE</th> + <th scope="col">NUCLEOTIDE</th> + <th scope="col">CONSEQUENCE</th> + <th scope="col">IMPACT</th> + <th scope="col">PATHWAY</th> + </tr> + </thead> + <tbody> + + <tr> + <td>Chromosome</td> + <td>Rv0014c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0014c" target="_blank" + rel="noreferrer noopener">GENE_Rv0014c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A15890..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A15890..None" + target="_blank" rel="noreferrer noopener">15890</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.1581C>T</td> + <td>p.Ser527Ser</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv0127</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0127" target="_blank" + rel="noreferrer noopener">GENE_Rv0127</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A154990..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A154990..None" + target="_blank" rel="noreferrer noopener">154990</a> + </td> + <td>G</td> + <td>T</td> + <td>protein_coding</td> + <td>c.759G>T</td> + <td>p.Arg253Arg</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv0284</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0284" target="_blank" + rel="noreferrer noopener">GENE_Rv0284</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A346693..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A346693..None" + target="_blank" rel="noreferrer noopener">346693</a> + </td> + <td>G</td> + <td>T</td> + <td>protein_coding</td> + <td>c.1059G>T</td> + <td>p.Ser353Ser</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv0372c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0372c" target="_blank" + rel="noreferrer noopener">GENE_Rv0372c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A449194..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A449194..None" + target="_blank" rel="noreferrer noopener">449194</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.192C>T</td> + <td>p.Gly64Gly</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv0411c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0411c" target="_blank" + rel="noreferrer noopener">GENE_Rv0411c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A497491..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A497491..None" + target="_blank" rel="noreferrer noopener">497491</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.810C>T</td> + <td>p.Asp270Asp</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv0667</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0667" target="_blank" + rel="noreferrer noopener">GENE_Rv0667</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A761110..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A761110..None" + target="_blank" rel="noreferrer noopener">761110</a> + </td> + <td>A</td> + <td>T</td> + <td>protein_coding</td> + <td>c.1304A>T</td> + <td>p.Asp435Val</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv0715</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0715" target="_blank" + rel="noreferrer noopener">GENE_Rv0715</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A811753..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A811753..None" + target="_blank" rel="noreferrer noopener">811753</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.12C>T</td> + <td>p.His4His</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv1391</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1391" target="_blank" + rel="noreferrer noopener">GENE_Rv1391</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1565566..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1565566..None" + target="_blank" rel="noreferrer noopener">1565566</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.126C>T</td> + <td>p.Pro42Pro</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv1630</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1630" target="_blank" + rel="noreferrer noopener">GENE_Rv1630</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1834177..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1834177..None" + target="_blank" rel="noreferrer noopener">1834177</a> + </td> + <td>A</td> + <td>C</td> + <td>protein_coding</td> + <td>c.636A>C</td> + <td>p.Arg212Arg</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv1640c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1640c" target="_blank" + rel="noreferrer noopener">GENE_Rv1640c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1849051..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1849051..None" + target="_blank" rel="noreferrer noopener">1849051</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.2985G>A</td> + <td>p.Pro995Pro</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv2231c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2231c" target="_blank" + rel="noreferrer noopener">GENE_Rv2231c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2505085..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2505085..None" + target="_blank" rel="noreferrer noopener">2505085</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.615C>T</td> + <td>p.Ala205Ala</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv2268c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2268c" target="_blank" + rel="noreferrer noopener">GENE_Rv2268c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2543395..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2543395..None" + target="_blank" rel="noreferrer noopener">2543395</a> + </td> + <td>T</td> + <td>C</td> + <td>protein_coding</td> + <td>c.882A>G</td> + <td>p.Glu294Glu</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv2357c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2357c" target="_blank" + rel="noreferrer noopener">GENE_Rv2357c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2640807..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2640807..None" + target="_blank" rel="noreferrer noopener">2640807</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.258C>T</td> + <td>p.Val86Val</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv2472</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2472" target="_blank" + rel="noreferrer noopener">GENE_Rv2472</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2775361..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2775361..None" + target="_blank" rel="noreferrer noopener">2775361</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.90C>T</td> + <td>p.Arg30Arg</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv2483c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2483c" target="_blank" + rel="noreferrer noopener">GENE_Rv2483c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2789798..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2789798..None" + target="_blank" rel="noreferrer noopener">2789798</a> + </td> + <td>G</td> + <td>T</td> + <td>protein_coding</td> + <td>c.1225C>A</td> + <td>p.Arg409Arg</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3109</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3109" target="_blank" + rel="noreferrer noopener">GENE_Rv3109</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3477942..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3477942..None" + target="_blank" rel="noreferrer noopener">3477942</a> + </td> + <td>A</td> + <td>G</td> + <td>protein_coding</td> + <td>c.294A>G</td> + <td>p.Thr98Thr</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3210c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3210c" target="_blank" + rel="noreferrer noopener">GENE_Rv3210c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None" + target="_blank" rel="noreferrer noopener">3587446</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.94C>T</td> + <td>p.Leu32Leu</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3799c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank" + rel="noreferrer noopener">GENE_Rv3799c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None" + target="_blank" rel="noreferrer noopener">4254431</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.1518C>T</td> + <td>p.Asp506Asp</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3799c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank" + rel="noreferrer noopener">GENE_Rv3799c</a> + </td> + <td> + <p>NA</p> + </td> + <td>True</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None" + target="_blank" rel="noreferrer noopener">4254477</a> + </td> + <td>T</td> + <td>C</td> + <td>protein_coding</td> + <td>c.1472A>G</td> + <td>p.His491Arg</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + </tbody> + <tfoot class="thead-light"> + <tr> + <th scope="col">CHR</th> + <th scope="col">GENE</th> + <th scope="col">LOCUS</th> + <th scope="col">PRODUCT</th> + <th scope="col">TYPE</th> + <th scope="col">EFFECT</th> + <th scope="col">POS</th> + <th scope="col">REF</th> + <th scope="col">ALT</th> + <th scope="col">BIOTYPE</th> + <th scope="col">NUCLEOTIDE</th> + <th scope="col">CONSEQUENCE</th> + <th scope="col">IMPACT</th> + <th scope="col">PATHWAY</th> + </tr> + </tfoot> + </table> +</div> +</main> +<div class="mt-5"> </div> <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">