c7aab3a42e921c2d7019321969409bf0353abe3e
lrnassar
  Fri Mar 28 16:44:45 2025 -0700
Making MANE a default hg38 track due to popular use, and nesting the two patch sequence tracks into one composite so we can use the hideEmptySubtracks setting. The tracks are rarely used and this allows us to open up virtual real estate while still displaying them in important regions where they are vauable. Refs #35326

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+<h2>Description</h2>
+<p>
+These tracks show the two types of patch sequences from the <a 
+href="https://www.ncbi.nlm.nih.gov/grc" target=_blank>Genome Reference Consortium
+(GRC)</a> patch releases:</p>
+
+<h3>Fix Patches</h3>
+<p>
+This track shows alignments of fix patch sequences to
+main chromosome sequences in the reference genome assembly.
+When errors are corrected in the reference genome assembly, the
+<a href="https://www.ncbi.nlm.nih.gov/grc" target=_blank>Genome Reference Consortium
+(GRC)</a> adds fix patch sequences containing the corrected regions.
+This strikes a balance between providing the most complete and correct genome
+sequence, while maintaining stable chromosome coordinates for the original assembly
+sequences.
+</p>
+<p>
+Fix patches are often associated with incident reports displayed in the GRC Incidents
+track.
+</p>
+
+<h3>Alt Haplotypes</h3>
+<p>
+This track shows alignments of alternate locus (also known as &quot;alternate haplotype&quot;)
+reference sequences to main chromosome sequences in the reference genome assembly.
+Some loci in the genome are highly variable, with sets of variants that tend
+to segregate into distinct haplotypes.
+Only one haplotype can be included in a reference assembly chromosome sequence.
+Instead of providing a separate complete chromosome sequence for each haplotype,
+which could cause confusion with divergent chromosome coordinates and
+ambiguity about which sequence is the official reference, the
+<a href="https://www.ncbi.nlm.nih.gov/grc" target=_blank>Genome Reference Consortium
+(GRC)</a> adds alternate locus sequences, ranging from tens of thousands of bases
+up to low millions of bases in size, to represent the distinct haplotypes.  
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+<p>
+Both tracks follow the display conventions for
+<a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">
+PSL alignment tracks</a>.
+Mismatching bases are highlighted in red.
+Several types of alignment gap may also be colored;
+for more information, see
+<a href="../goldenPath/help/hgIndelDisplay.html" target="_blank">
+Alignment Insertion/Deletion Display Options</a>.
+</p>
+<p>
+By default, the tracks are only visible when there are items in the view window.
+This can be disabled by the checkbox <b>Hide empty subtracks</b>.</p>
+
+<h2>Credits</h2>
+<p>
+The alignments were provided by NCBI as GFF files and translated into the PSL
+representation for browser display by UCSC.
+</p>