23bea12e98867f3cd6b931d0537c68b57a2f0503
gperez2
  Thu Jul 31 10:54:57 2025 -0700
Incorporating Lou's feedback to bedMethyl.html and announcing the bedMethyl/bigMethyl type, refs #36002

diff --git src/hg/htdocs/goldenPath/help/bedMethyl.html src/hg/htdocs/goldenPath/help/bedMethyl.html
index 35b57aeb213..35624070b35 100755
--- src/hg/htdocs/goldenPath/help/bedMethyl.html
+++ src/hg/htdocs/goldenPath/help/bedMethyl.html
@@ -22,31 +22,32 @@
 <li>Canonical calls: Number of calls with a canonical base
 <li>Other modification calls: Number of calls with a modified base, other modifications
 <li>Reads with a deletion: Number of reads with a deletion at this reference position
 <li>Low-confidence calls: Number of calls where the probability of the call was below the threshold
 <li>Reads with a base mismatch: Number of reads with a base other than the canonical base for this modification
 <li>Reads with no modification call: Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call
 </ul>
 
 <p class="text-center">
 <img "1080" height="148" src="../../images/bedMethylEx.jpg">
 </p>
 
 <p>The items are colored from <b><font color="#0000FF">0%</font></b> 
 methylated modified (blue) to
 <b><font color="#FF0000">100%</font></b> (red). Hovering over an item or
-clicking it shows the additional details found in bedMethyl.</p> 
+clicking it shows the additional details found in bedMethyl. Methylation calls are shown
+separately for CpG sites (<b>m</b>) and non-CpG (CHG/CHH) sites (<b>h</b>).</p>
 
 <a name=bedMethyl></a>
 <h2>Creating a bedMethyl custom track</h2>
 <a name="example1"></a>
 <h3>Example #1</h3>
 <p>
 In this example, you will create a bedMethyl custom track using bedMethyl data for the hg38 assembly.</p>
 <ol>
    <li>Paste the following track line into the
        <a href="../../cgi-bin/hgCustom?db=hg19">custom track management 
    page</a> for the human assembly hg38.
 
    <pre><code>
 
 track type=bedMethyl name=&quot;bedmethyl example&quot; description=&quot;bedMethyl custom track&quot; visibility=&quot;pack&quot;