f20b31ea40c4fd47327f892ebca33a3c63e8f5b4
lrnassar
  Thu Jun 15 13:33:34 2023 -0700
Adding a plug to rearrangement docs from the BLAT desc page, refs #31241

diff --git src/hg/htdocs/goldenPath/help/hgUserPsl.html src/hg/htdocs/goldenPath/help/hgUserPsl.html
index c719b1c..eb8fe53 100644
--- src/hg/htdocs/goldenPath/help/hgUserPsl.html
+++ src/hg/htdocs/goldenPath/help/hgUserPsl.html
@@ -1,28 +1,30 @@
 <h2>Description</h2>
 <p>
-This track shows the BLAT alignments of your sequence(s) to the genome assembly. In the Genome 
+This track shows the BLAT alignments of your sequence(s) to the genome assembly. The data display can 
+also be toggled to a density graph, or <a href="/goldenPath/help/chain.html#rearrangement" 
+target="_blank">rearrangement display</a>. In the Genome 
 Browser, alignments of nucleotides use color to highlight differences as follows:
 <ul>
   <li>
   <font color="red"><strong>red:</strong></font> Genome and query sequence have different bases at 
   this position.</li>
   <li>
   <font color="orange"><strong>orange:</strong></font> The query sequence has an insertion (or 
   genome has a deletion / alignment gap) at this point.</li>
   <li>
   <font color="#9214FF"><strong>purple:</strong></font> The query sequence extends beyond the end 
   of the alignment.</li>
   <li>
   <font color="green"><strong>green:</strong></font> The query sequence appears to have a polyA tail
    that is not aligned to the genome.</li>
 </ul>
 <p>
 Also, when the alignment has gaps in both the genome and query sequence, double horizontal lines are
 drawn.</p>
 
 <h2>Credits</h2>
 <p>
 This track was generated by 
 <a href="mailto:&#107;&#101;&#110;t&#64;&#115;&#111;e.&#117;&#99;&#115;&#99;.&#101;&#100;&#117;">Jim Kent</a> 
 of the UCSC Genome Bioinformatics Group.</p>