<!DOCTYPE html>


<html>
<head>
{% include "chlamdb/header.html" %}
{% load custom_tags %}
</head>

<body>
  <div class="container-fluid" id="main_container">
    <div class="row">
      <div id="wrapper">
        <div id="page-content-wrapper">
          {% include "chlamdb/comparison_header.html" %}


          {% if show_results %}
            <div class="row" style="background-color: rgba(245, 245, 245, 0.986)" >
              <div class="panel panel-success" style="margin: 1em;">
                <div class="panel-heading" >
                  <h5 class="panel-title">Help to interpret the results</h5>
                </div>
                <p style="margin: 10px 10px 10px 10px">
                  The table displays results for all {{object_name_plural}} that passed filtering (q-value<{{qval_threshold}}).
                  <br><br>
                  The significance of the association for each {{object_name}} is reported with (see <a href="https://github.com/MrTomRod/scoary-2/wiki/Understanding-the-p-values">Scoary-2</a> for more information):
                  <ul style="margin-left: 20px; list-style-type:disc;" >
                    <li><b>Sensitivity</b>: probability of trait being present if gene is present</li>
                    <li><b>Specificity</b>: probability of trait being absent if gene is absent</li>
                    <li><b>p-value</b>: p-value of Fisher's test</li>
                    <li><b>q-value</b>: q-value of Fisher's test, i.e. the expected False Discovery Rate</li>
                    <li><b>Empirical p-value</b>: Calculated from the best pairwise p-value 500 random permutations of the phenotype.</li>
                    <li><b>Best pairwise p-value</b>: Best p-value obtained from pairwise comparisons to take population structure into account.</li>
                    <li><b>Worst pairwise p-value</b>: Worst p-value obtained from pairwise comparisons to take population structure into account.</li>
                    <li><b>fq*ep</b>: Product of Fisher's q-value with the empirical p-value.</li>
                  </ul>
                </p>
              </div>
              {% include "chlamdb/result_tabs.html" %}
            </div>
          {% endif %}
        </div>
      </div>
    </div>
  </div>

</body>
{% include "chlamdb/style_menu.html" %}
</html>
