726a4c9c82592c662ae6b8c715e67b783c95beb3
angie
  Mon Nov 18 13:45:42 2019 -0800
Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped.  refs #23283

diff --git src/hg/makeDb/trackDb/human/dbSnp153Composite.html src/hg/makeDb/trackDb/human/dbSnp153Composite.html
index a2dba17..5f622ea 100644
--- src/hg/makeDb/trackDb/human/dbSnp153Composite.html
+++ src/hg/makeDb/trackDb/human/dbSnp153Composite.html
@@ -335,59 +335,78 @@
   </tr>
   <tr>
     <td>classMismatch</td>
     <td class="number">5995</td>
     <td class="number">6206</td>
     <td>Variation class/type is inconsistent with alleles mapped to this genome assembly.</td>
   </tr>
   <tr>
     <td>clusterError</td>
     <td class="number">114685</td>
     <td class="number">128109</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>freqIncomplete</td>
+    <td class="number">3922</td>
+    <td class="number">4673</td>
+    <td>At least one project reported counts for only one allele which implies that at
+      least one allele is missing from the report;
+      that project's frequency data are ignored.</td>
+  </tr>
+  <tr>
     <td>freqIsAmbiguous</td>
     <td class="number">7656</td>
     <td class="number">7756</td>
     <td>At least one allele reported by at least one project that reports frequencies
       contains an IUPAC ambiguous base.</td>
   </tr>
   <tr>
+    <td>freqNotMapped</td>
+    <td class="number">2685</td>
+    <td class="number">6590</td>
+    <td>At least one project reported allele frequencies relative to a different assembly;
+      However, dbSNP does not include a mapping of this variant to that assembly, which
+      implies a problem with mapping the variant across assemblies.  The mapping on this
+      assembly may have an issue; evaluate carefully vs. original submissions, which you
+      can view by clicking through to dbSNP above.</td>
+  </tr>
+  <tr>
     <td>freqNotRefAlt</td>
     <td class="number">17684</td>
     <td class="number">32150</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">562157</td>
     <td class="number">132051</td>
     <td>This variant has been mapped to more than one distinct genomic location.</td>
   </tr>
   <tr>
     <td>otherMapErr</td>
     <td class="number">113416</td>
     <td class="number">203580</td>
     <td>At least one other mapping of this variant has erroneous coordinates.
       The mapping(s) with erroneous coordinates are excluded from this track
       and are included in the Map Err subtrack.  Sometimes despite this mapping
       having legal coordinates, there may still be an issue with this mapping's
       coordinates and alleles; you may want to click through to dbSNP to compare
       the initial submission's coordinates and alleles.
+      In hg19, 55453 distinct rs IDs are affected; in hg38, 86636.
   </tr>
 </table>
 
 
 <h2>Data Sources and Methods</h2>
 <p>
 dbSNP has collected genetic variant reports from researchers worldwide for 
 <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2019/10/07/dbsnp-celebrates-20-years/"
    target=_blank>over 20 years</a>.
 Since the advent of next-generation sequencing methods and the population sequencing efforts
 that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline,
 web infrastructure, and download files.
 (Holmes <em>et al.</em>)
 The same challenges of exponential growth affected UCSC's presentation of dbSNP variants,
 so we have taken the opportunity to change our internal representation and import pipeline.