<!DOCTYPE html>
<html>
<head>
  <meta charset="utf-8">
  <title>MiModD Variant Report</title>
  <link rel="stylesheet" type="text/css" href="variant_report.css">
  <base target="_blank">
</head>
<body>
<div id="main_container" style="position: relative;">
<div id="no_style_warning" style="background-color: #F5A9A9; border: 1px solid #F78181; position: absolute;">
  <hr>
  <p><strong>This page will look so much nicer when it's styled!</strong><p>
  <p>If you are viewing this through Galaxy, then the Galaxy server is blocking
  the style information accompanying the page. In this case, we recommend you
  to: </p>
  <ol>
    <li>download the dataset,</li>
    <li>extract the <b>variant_report.html</b> file from the resulting zip archive and</li>
    <li>open this local file with your browser.</li>
  </ol>
  <hr>
</div>
<div class="box">
<footer>
<span class="info" tabindex="-1"><strong>show table legend <<</strong></span>
<div id="table_legend">
  <h1>Table Legend</h1>
  <table>
    <caption>Genotype qualities are indicated using the color scheme:</caption>
    <thead>
      <tr>
        <th rowspan="2">Genotype</th>
        <th colspan="5">Genotype Quality Range</th>
      </tr>
      <tr>
        <th>0 - 6</th>
        <th>6 - 46</th>
        <th>47 - 70</th>
        <th>71 - 92</th>
        <th> >=92</th>
      </tr>
    </thead>
    <tbody>
      <tr>
        <td>homozygous ref</td>
        <td class="gt" gt="ref" level="1">    </td>
        <td class="gt" gt="ref" level="2">    </td>
        <td class="gt" gt="ref" level="3">    </td>
        <td class="gt" gt="ref" level="4">    </td>
        <td class="gt" gt="ref" level="5">    </td>
      </tr>
      <tr>
        <td>heterozygous</td>
        <td class="gt" gt="het" level="1">    </td>
        <td class="gt" gt="het" level="2">    </td>
        <td class="gt" gt="het" level="3">    </td>
        <td class="gt" gt="het" level="4">    </td>
        <td class="gt" gt="het" level="5">    </td>
      </tr>
      <tr>
        <td>homozygous mutant</td>
        <td class="gt" gt="mut" level="1">    </td>
        <td class="gt" gt="mut" level="2">    </td>
        <td class="gt" gt="mut" level="3">    </td>
        <td class="gt" gt="mut" level="4">    </td>
        <td class="gt" gt="mut" level="5">    </td>
      </tr>
    </tbody>
  </table>
  <div>
    <span class="caption">Effect impact color scheme:</span>
    <ul>
      <li class="eff" level="MODIFIER">MODIFIER</li>
      <li class="eff" level="HIGH">HIGH</li>
      <li class="eff" level="MODERATE">MODERATE</li>
      <li class="eff" level="LOW" style="margin-right: 0em">LOW</li>
    </ul>
  </div>
</div>
</footer>
<table id="data_table">
<thead>
  <tr>
    <th>Location</th>
    <th>Sample Pattern</th>
    <th>Affected Genes</th>
    <th>Transcripts</th>
    <th>Effects</th>
  </tr>
</thead>
<!-- BREAK -->
<tbody tabindex="{uid}">
<!-- BREAK -->
  <tr>
    {location}
    {sample_specs}
    {gene}
    {transcript}
    {effects}
  </tr>
<!-- BREAK -->
  <tr class="detail"><td colspan="5">
    <table>
      <caption>per-sample characteristics</caption>
        <thead><tr><th>sample</th><th>genotype</th><th>observed reads/allele</th><th>genotype call quality</th></tr></thead>
        <tbody>
          {per_sample_details}
        </tbody>
    </table>
    <ul class="legend" header="allele code:">
      {allele_legend}
    </ul>
  </td></tr>

<!-- BREAK -->
</tbody>
<!-- BREAK -->
</table>
</div>
</div>
</body>
</html>
