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
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            <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>
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