Mercurial > repos > iuc > tbvcfreport
view test-data/rif_resistant_variants_report_with_lineage.html @ 4:9793bc5d741b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit a8fe4cf3a77ffb0334533cccb57b7af5f7f89e3b
| author | iuc |
|---|---|
| date | Fri, 07 Jun 2024 14:29:45 +0000 |
| parents | 42818629ec4c |
| children |
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<!DOCTYPE html> <html> <head> <title></title> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous"> <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"> <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.bootstrap4.min.css"> <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.dataTables.min.css"> </head> <body> <div class="container"> <div class="row"> <h2 class="mt-5"> 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"> <thead class="thead-light"> <tr> <th scope="col">Lineage</th> <th scope="col">Family</th> <th scape="col">Spoligotype</th> <th scope="col">RD</th> <th scope="col">Agreement</th> </tr> </thead> <tbody> <tr> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> </tbody> </table> </div> <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"> </script> 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