3d835ba54509284ec08b63dc527bd114c9467afc
angie
  Tue Nov 12 10:55:41 2019 -0800
Update counts of diffMajor, refIs{Minor,Rare,Singleton}, freqNotRefAlt after fixing VCF allele normalization in dbSnpJsonToTab.  refs #23283

diff --git src/hg/makeDb/trackDb/human/dbSnp153Composite.html src/hg/makeDb/trackDb/human/dbSnp153Composite.html
index 9c771d1..4df4a35 100644
--- src/hg/makeDb/trackDb/human/dbSnp153Composite.html
+++ src/hg/makeDb/trackDb/human/dbSnp153Composite.html
@@ -216,32 +216,32 @@
     <td>commonAll</td>
     <td class="number">12178426</td>
     <td class="number">12430253</td>
     <td>Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all
       projects reporting frequencies.</td>
   </tr>
   <tr>
     <td>commonSome</td>
     <td class="number">20534330</td>
     <td class="number">20893174</td>
     <td>Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all,
       projects reporting frequencies.</td>
   </tr>
   <tr>
     <td>diffMajor</td>
-    <td class="number">1378125</td>
-    <td class="number">1399317</td>
+    <td class="number">1377402</td>
+    <td class="number">1398591</td>
     <td>Different frequency sources have different major alleles.</td>
   </tr>
   <tr>
     <td>overlapDiffClass</td>
     <td class="number">106940656</td>
     <td class="number">109838613</td>
     <td>This variant overlaps another variant with a different type/class.</td>
   </tr>
   <tr>
     <td>overlapSameClass</td>
     <td class="number">16890303</td>
     <td class="number">17228657</td>
     <td>This variant overlaps another with the same type/class but different start/end.</td>
   </tr>
   <tr>
@@ -271,44 +271,44 @@
 <p>
 while others may indicate that the reference genome contains a rare variant or sequencing issue:
 </p>
 <table class="descTbl">
   <tr><th>keyword in data file (dbSnp153.bb)</th>
     <th># in hg19</th><th># in hg38</th><th>description</th></tr>
   <tr>
     <td>refIsAmbiguous</td>
     <td class="number">101</td>
     <td class="number">111</td>
     <td>The reference genome allele contains an IUPAC ambiguous base
       (e.g. 'R' for 'A or G', or 'N' for 'any base').</td>
   </tr>
   <tr>
     <td>refIsMinor</td>
-    <td class="number">3277722</td>
-    <td class="number">3364788</td>
+    <td class="number">3269451</td>
+    <td class="number">3356557</td>
     <td>The reference genome allele is not the major allele in at least one project.</td>
   </tr>
   <tr>
     <td>refIsRare</td>
-    <td class="number">142937</td>
-    <td class="number">166192</td>
+    <td class="number">135265</td>
+    <td class="number">158562</td>
     <td>The reference genome allele is rare (i.e. allele frequency < 1%).</td>
   </tr>
   <tr>
     <td>refIsSingleton</td>
-    <td class="number">44382</td>
-    <td class="number">56491</td>
+    <td class="number">36709</td>
+    <td class="number">48859</td>
     <td>The reference genome allele has never been observed in a population sequencing project
       reporting frequencies.</td>
   </tr>
   <tr>
     <td>refMismatch</td>
     <td class="number">4</td>
     <td class="number">33</td>
     <td>The reference genome allele reported by dbSNP differs from the GenBank assembly sequence.
       This is very rare and in all cases observed so far, the GenBank assembly has an 'N'
       while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'.</td>
   </tr>
 </table>
 <p>
 and others may indicate an anomaly or problem with the variant data:
 </p>
@@ -333,32 +333,32 @@
     <td>clusterError</td>
     <td class="number">113678</td>
     <td class="number">126973</td>
     <td>This variant has the same start, end and class as another variant;
       they probably should have been merged into one variant.</td>
   </tr>
   <tr>
     <td>freqIsAmbiguous</td>
     <td class="number">7649</td>
     <td class="number">7749</td>
     <td>At least one allele reported by at least one project that reports frequencies
       contains an IUPAC ambiguous base.</td>
   </tr>
   <tr>
     <td>freqNotRefAlt</td>
-    <td class="number">25413</td>
-    <td class="number">39038</td>
+    <td class="number">16950</td>
+    <td class="number">30615</td>
     <td>At least one allele reported by at least one project that reports frequencies
       does not match any of the reference or alternate alleles listed by dbSNP.</td>
   </tr>
   <tr>
     <td>multiMap</td>
     <td class="number">561309</td>
     <td class="number">132015</td>
     <td>This variant has been mapped to more than one distinct genomic location.</td>
   </tr>
 </table>
 
 
 <h2>Data Sources and Methods</h2>
 <p>
 dbSNP has collected genetic variant reports from researchers worldwide for