Mercurial > repos > iuc > tbvcfreport
view test-data/vcf_with_no_protein_report.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 |
line wrap: on
line source
<!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"> vcf_with_no_protein Report </h2> </div> <hr> <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>Rv3753c</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3753c" target="_blank" rel="noreferrer noopener">Rv3753c</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=O69720" target="_blank" rel="noreferrer noopener">O69720</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..None" target="_blank" rel="noreferrer noopener">4200220</a> </td> <td>G</td> <td>A</td> <td>protein_coding</td> <td>c.2C>T</td> <td>p.Thr1Met</td> <td>MODERATE</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3756c</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3756c" target="_blank" rel="noreferrer noopener">Rv3756c</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=O69722" target="_blank" rel="noreferrer noopener">O69722</a> </td> <td>True</td> <td>synonymous_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..None" target="_blank" rel="noreferrer noopener">4202383</a> </td> <td>C</td> <td>A</td> <td>protein_coding</td> <td>c.231G>T</td> <td>p.Val77Val</td> <td>LOW</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu02010" target="_blank" rel="noreferrer noopener">ABC transporters</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3759c</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3759c" target="_blank" rel="noreferrer noopener">Rv3759c</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=O69725" target="_blank" rel="noreferrer noopener">O69725</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..None" target="_blank" rel="noreferrer noopener">4205120</a> </td> <td>G</td> <td>A</td> <td>protein_coding</td> <td>c.254C>T</td> <td>p.Pro85Leu</td> <td>MODERATE</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu02010" target="_blank" rel="noreferrer noopener">ABC transporters</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3764c</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3764c" target="_blank" rel="noreferrer noopener">Rv3764c</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=O69729" target="_blank" rel="noreferrer noopener">O69729</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..None" target="_blank" rel="noreferrer noopener">4210876</a> </td> <td>C</td> <td>T</td> <td>protein_coding</td> <td>c.134G>A</td> <td>p.Arg45His</td> <td>MODERATE</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3769</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3769" target="_blank" rel="noreferrer noopener">Rv3769</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P72036" target="_blank" rel="noreferrer noopener">P72036</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4214747..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4214747..None" target="_blank" rel="noreferrer noopener">4214747</a> </td> <td>C</td> <td>T</td> <td>protein_coding</td> <td>c.133C>T</td> <td>p.His45Tyr</td> <td>MODERATE</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3770c</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3770c" target="_blank" rel="noreferrer noopener">Rv3770c</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P72037" target="_blank" rel="noreferrer noopener">P72037</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4215484..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4215484..None" target="_blank" rel="noreferrer noopener">4215484</a> </td> <td>C</td> <td>G</td> <td>protein_coding</td> <td>c.292G>C</td> <td>p.Ala98Pro</td> <td>MODERATE</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3772</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3772" target="_blank" rel="noreferrer noopener">Rv3772</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P9WML5" target="_blank" rel="noreferrer noopener">P9WML5</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4217557..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4217557..None" target="_blank" rel="noreferrer noopener">4217557</a> </td> <td>G</td> <td>A</td> <td>protein_coding</td> <td>c.424G>A</td> <td>p.Ala142Thr</td> <td>MODERATE</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00400" target="_blank" rel="noreferrer noopener">Phenylalanine, tyrosine and tryptophan biosynthesis</a> </small> </p> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00360" target="_blank" rel="noreferrer noopener">Phenylalanine metabolism</a> </small> </p> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00340" target="_blank" rel="noreferrer noopener">Histidine metabolism</a> </small> </p> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00350" target="_blank" rel="noreferrer noopener">Tyrosine metabolism</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3777</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3777" target="_blank" rel="noreferrer noopener">Rv3777</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P72043" target="_blank" rel="noreferrer noopener">P72043</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4223172..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4223172..None" target="_blank" rel="noreferrer noopener">4223172</a> </td> <td>C</td> <td>T</td> <td>protein_coding</td> <td>c.479C>T</td> <td>p.Ala160Val</td> <td>MODERATE</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3785</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3785" target="_blank" rel="noreferrer noopener">Rv3785</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P9WKX1" target="_blank" rel="noreferrer noopener">P9WKX1</a> </td> <td>True</td> <td>synonymous_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4232327..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4232327..None" target="_blank" rel="noreferrer noopener">4232327</a> </td> <td>G</td> <td>A</td> <td>protein_coding</td> <td>c.1008G>A</td> <td>p.Arg336Arg</td> <td>LOW</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3792</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3792" target="_blank" rel="noreferrer noopener">Rv3792</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P9WN03" target="_blank" rel="noreferrer noopener">P9WN03</a> </td> <td>True</td> <td>synonymous_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4238963..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4238963..None" target="_blank" rel="noreferrer noopener">4238963</a> </td> <td>C</td> <td>T</td> <td>protein_coding</td> <td>c.1032C>T</td> <td>p.His344His</td> <td>LOW</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3792</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3792" target="_blank" rel="noreferrer noopener">Rv3792</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P9WN03" target="_blank" rel="noreferrer noopener">P9WN03</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4239274..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4239274..None" target="_blank" rel="noreferrer noopener">4239274</a> </td> <td>C</td> <td>G</td> <td>protein_coding</td> <td>c.1343C>G</td> <td>p.Pro448Arg</td> <td>MODERATE</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3793</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3793" target="_blank" rel="noreferrer noopener">Rv3793</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P9WNL5" target="_blank" rel="noreferrer noopener">P9WNL5</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4240671..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4240671..None" target="_blank" rel="noreferrer noopener">4240671</a> </td> <td>T</td> <td>C</td> <td>protein_coding</td> <td>c.809T>C</td> <td>p.Ile270Thr</td> <td>MODERATE</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00571" target="_blank" rel="noreferrer noopener">Lipoarabinomannan (LAM) biosynthesis</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3795</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3795" target="_blank" rel="noreferrer noopener">Rv3795</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7" target="_blank" rel="noreferrer noopener">P9WNL7</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247429..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247429..None" target="_blank" rel="noreferrer noopener">4247429</a> </td> <td>A</td> <td>G</td> <td>protein_coding</td> <td>c.916A>G</td> <td>p.Met306Val</td> <td>MODERATE</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3795</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3795" target="_blank" rel="noreferrer noopener">Rv3795</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7" target="_blank" rel="noreferrer noopener">P9WNL7</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..None" target="_blank" rel="noreferrer noopener">4247646</a> </td> <td>C</td> <td>A</td> <td>protein_coding</td> <td>c.1133C>A</td> <td>p.Ala378Glu</td> <td>MODERATE</td> <td> <p> <small> <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> </small> </p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3797</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3797" target="_blank" rel="noreferrer noopener">Rv3797</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=O53577" target="_blank" rel="noreferrer noopener">O53577</a> </td> <td>True</td> <td>synonymous_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..None" target="_blank" rel="noreferrer noopener">4251297</a> </td> <td>C</td> <td>G</td> <td>protein_coding</td> <td>c.213C>G</td> <td>p.Gly71Gly</td> <td>LOW</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3798</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3798" target="_blank" rel="noreferrer noopener">Rv3798</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%3A4254290..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..None" target="_blank" rel="noreferrer noopener">4254290</a> </td> <td>T</td> <td>G</td> <td>protein_coding</td> <td>c.1298T>G</td> <td>p.Leu433Arg</td> <td>MODERATE</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3799c</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3799c" target="_blank" rel="noreferrer noopener">Rv3799c</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=O53578" target="_blank" rel="noreferrer noopener">O53578</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..None" target="_blank" rel="noreferrer noopener">4254478</a> </td> <td>G</td> <td>A</td> <td>protein_coding</td> <td>c.1471C>T</td> <td>p.His491Tyr</td> <td>MODERATE</td> <td> <p>NA</p> </td> </tr> <tr> <td>Chromosome</td> <td>Rv3801c</td> <td> <a href="https://explorer.sanbi.ac.za/gene?q=Rv3801c" target="_blank" rel="noreferrer noopener">Rv3801c</a> </td> <td> <a href="https://explorer.sanbi.ac.za/search?q=O53580" target="_blank" rel="noreferrer noopener">O53580</a> </td> <td>True</td> <td>missense_variant</td> <td> <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..None" target="_blank" rel="noreferrer noopener">4261499</a> </td> <td>A</td> <td>G</td> <td>protein_coding</td> <td>c.1568T>C</td> <td>p.Val523Ala</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> <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js" integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous"> </script> <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js" integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous"> </script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/buttons/1.5.2/js/dataTables.buttons.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.bootstrap4.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.flash.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.html5.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.print.min.js"></script> <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.colVis.min.js"></script> <script type="text/javascript" language="javascript" class="init"> $(function () { var table = $('#vcfreport').DataTable({ lengthChange: false, buttons: [{ extend: 'csv', text: 'Download CSV', filename: 'vcf_with_no_protein' }] }); table.buttons().container().appendTo('#vcfreport_wrapper .col-md-6:eq(0)'); }); </script> </div> </body> </html>