6b4f1b0a4fb33ae0af9c930dbf479497f7b07593
max
  Wed Aug 21 02:52:48 2019 -0700
adding note about missing chrM annotations on clinvar hg19 to clinvar docs page, result of email from Conner

diff --git src/hg/makeDb/trackDb/human/clinvar.html src/hg/makeDb/trackDb/human/clinvar.html
index 3e61a74..c62cb1b 100644
--- src/hg/makeDb/trackDb/human/clinvar.html
+++ src/hg/makeDb/trackDb/human/clinvar.html
@@ -50,30 +50,39 @@
 <B><font color="blue">blue for gain</font></b>.
 </p>
 
 <p>
 Entries in the ClinVar short variants track are shaded by clinical annotation:
 <b><font color="red">red for pathogenic</font></b>,
 <B><font color="#888">dark grey for uncertain significance or not provided</font></b> and
 <B><font color="green">green for benign</font></b>.
 </p>
 
 <p>
 The score of the variants is the number of "stars" in ClinVar. On the track configuration page (above), you can filter the track to show only variants with more than a certain number of stars. For more information on the star rating, see the <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/"
 target="_blank">ClinVar documentation</a>.
 </p>
 
+<p>On the human assembly hg19, no variants on the mitochondrial genome are
+shown, as the mitochondrial genome was not part of the human genome when it was
+released. The version of "chrM" that was selected from Genbank by UCSC when 
+the hg19 assembly was packaged is different than the version added by NCBI when
+they added an "MT" sequence later. Since the mitochondrial sequence differs,
+the variant positions cannot be converted reliably.
+</p>
+
+
 <h2>Data updates</h2>
 <p>ClinVar publishes a new release on the 
 <a href="https://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=ClinVarNews">first Thursday every month</a> 
 and this track is updated automatically at most six days 
 later. The exact date of our last update is shown when you click onto any variant. 
 You can find the previous versions of the track organized by month on our
 downloads server in the 
 <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/archive/clinvar/" target="_blank">archive</a>
 directory. To access one of these previous versions, paste the URL to one of
 the older files into our "Custom tracks" box.</p>
 
 <H2>Data access</H2>
 <p>
 The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>
 or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>.