f72322167bc143b5d6e9d6b81e6a0d0d0765b64c
max
  Wed Mar 11 01:56:00 2020 -0700
adding note about mitochondrial genome on hg19, but commented out. QA should uncomment the note with the release of #24648. refs #24648

diff --git src/hg/makeDb/trackDb/human/clinvar.html src/hg/makeDb/trackDb/human/clinvar.html
index 93ce778..161aa68 100644
--- src/hg/makeDb/trackDb/human/clinvar.html
+++ src/hg/makeDb/trackDb/human/clinvar.html
@@ -42,45 +42,47 @@
 Until October 2017, all variants with the ClinVar types copy number gain/loss
 and DbVar "nsv" accessions were put in the CNV category.  Due
 to the ClinVar type not capturing this information anymore, anything longer
 than 100bp is now considered a CNV.</p>
 
 <p>
 Entries in the ClinVar CNV track are colored
 <b><font color="red">red for loss</font></b> and
 <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="#ADD8E6">light blue for conflicting</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>For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a 
+mitochondrial genome "chrM" that was not the same as the one later used for most
+databases like ClinVar. As a result, we added the official mitochondrial genome
+in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other
+databases are shown on the mitochondrial genome called "chrMT".
 </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>