view test-data/vcf_with_no_protein_report.html @ 2:4934c0ac6197 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
author iuc
date Thu, 17 Mar 2022 07:33:00 +0000
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            <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">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>
        </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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..4200220&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..4200220"
                        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>snp</td>
                <td>synonymous_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..4202383&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..4202383"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..4205120&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..4205120"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..4210876&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..4210876"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4214747..4214747&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4214747..4214747"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4215484..4215484&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4215484..4215484"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4217557..4217557&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4217557..4217557"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4223172..4223172&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4223172..4223172"
                        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>snp</td>
                <td>synonymous_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4232327..4232327&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4232327..4232327"
                        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>snp</td>
                <td>synonymous_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4238963..4238963&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4238963..4238963"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4239274..4239274&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4239274..4239274"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4240671..4240671&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4240671..4240671"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247429..4247429&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247429..4247429"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..4247646&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..4247646"
                        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>snp</td>
                <td>synonymous_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..4251297&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..4251297"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254290..4254290&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..4254290"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..4254478&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..4254478"
                        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>snp</td>
                <td>missense_variant</td>
                <td>
                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..4261499&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..4261499"
                        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>
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