d base is 5mC. The primary base called by the read is included to help disambiguate the unmodified
patterns (<code>-,-</code>). All patterns recognized at a location will be reported in the bedMethyl output.</p>
<h3 id="definitions"><a class="header" href="#definitions">Definitions:</a></h3>
<ul>
<li>N<sub>pattern</sub> - Number of call-pairs passing filters that had the pattern and primary base in column 4. E.g. <code>m,-,C</code>
indicates the first base in the 5' to 3' direction is 5mC, the second base i