6e155ea5e313e29b07fb8068ceb1771cf77efab1
dschmelt
  Thu Oct 7 18:29:50 2021 -0700
Clarifying tStrand stands for target strand, etc. No RM

diff --git src/hg/htdocs/goldenPath/help/chain.html src/hg/htdocs/goldenPath/help/chain.html
index 3d0781a..a8ce96e 100755
--- src/hg/htdocs/goldenPath/help/chain.html
+++ src/hg/htdocs/goldenPath/help/chain.html
@@ -27,63 +27,63 @@
      16      0       2
      60      4       0
      10      0       4
      70</code></pre> 
 <p>
 <strong>Header Lines</strong> 
 <p>
 <pre><code>    <strong>chain</strong> <em>score</em> <em>tName</em> <em>tSize</em> <em>tStrand</em> <em>tStart</em> <em>tEnd</em> <em>qName</em> <em>qSize</em> <em>qStrand</em> <em>qStart</em> <em>qEnd</em> <em>id</em> </code></pre> 
 <p>
 The initial header line starts with the keyword <strong><code>chain</code></strong>, followed by 
 11 required attribute values, and ends with a blank line. The attributes include: 
 <ul> 
   <li> 
   <strong><code>score</code></em></strong> -- chain score</li>
   <li>
-  <strong><code>tName</code></strong> -- chromosome (reference sequence)</li>
+  <strong><code>tName</code></strong> -- chromosome (reference/target sequence)</li>
   <li>
-  <strong><code>tSize</code></strong> -- chromosome size (reference sequence)</li>
+  <strong><code>tSize</code></strong> -- chromosome size (reference/target sequence)</li>
   <li>
-  <strong><code>tStrand</code></strong> -- strand (reference sequence)</li>
+  <strong><code>tStrand</code></strong> -- strand (reference/target sequence)</li>
   <li>
-  <strong><code>tStart</code></strong> -- alignment start position (reference sequence)</li>
+  <strong><code>tStart</code></strong> -- alignment start position (reference/target sequence)</li>
   <li>
-  <strong><code>tEnd</code></strong> -- alignment end position (reference sequence)</li>
+  <strong><code>tEnd</code></strong> -- alignment end position (reference/target sequence)</li>
   <li>
   <strong><code>qName</code></strong> -- chromosome (query sequence)</li>
   <li>
   <strong><code>qSize</code></strong> -- chromosome size (query sequence)</li>
   <li>
   <strong><code>qStrand</code></strong> -- strand (query sequence)</li>
   <li>
   <strong><code>qStart</code></strong> -- alignment start position (query sequence)</li>
   <li>
   <strong><code>qEnd</code></strong> -- alignment end position (query sequence)</li>
   <li>
   <strong><code>id</code></strong> -- chain ID</li>
 </ul> 
 <p> 
 The alignment start and end positions are represented as zero-based half-open intervals. For 
 example, the first 100 bases of a sequence would be represented with start position = 0 and end 
 position = 100, and the next 100 bases would be represented as start position = 100 and end 
 position = 200. When the strand value is &quot;-&quot;, position coordinates are listed in terms of 
 the reverse-complemented sequence.</p> 
 <p>
 <strong>Alignment Data Lines</strong></p> 
 <p> 
 Alignment data lines contain three required attribute values:<p>
 <pre>    <em>size</em> <em>dt</em> <em>dq</em></pre>
 <ul> 
   <li> 
   <strong><code>size</code></strong> -- the size of the ungapped alignment</li>
   <li> 
   <strong><code>dt</code></strong> -- the difference between the end of this block and the beginning of 
-  the next block (reference sequence)</li>
+  the next block (reference/target sequence)</li>
   <li> 
   <strong><code>dq</code></strong> -- the difference between the end of this block and the beginning of 
   the next block (query sequence)</li>
 </ul> 
 <p> 
 NOTE: The last line of the alignment section contains only one number: the ungapped alignment size 
 of the last block.</p>
 
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