d379fe71f9062a15c3d0fe78ff64dd62edf9816e
dschmelt
  Thu Apr 1 15:18:59 2021 -0700
dbSnpArchive track commit, with version controlled data files for 3 assemblies, outlines in detail in refs #26719

diff --git src/hg/makeDb/trackDb/snp138.shared.html src/hg/makeDb/trackDb/snp138.shared.html
index fa7de35..07a81be 100644
--- src/hg/makeDb/trackDb/snp138.shared.html
+++ src/hg/makeDb/trackDb/snp138.shared.html
@@ -1,16 +1,16 @@
-The remainder of this page is identical on the following tracks:
+The remainder of this page is identical on the following tracks for all assemblies and versions:
 <UL>
   <LI>Common SNPs(138) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping
      only once to reference assembly.</LI>
 <!-- #if (db==hg19) #insert file="human/hg19/snp138FlaggedMention.html" -->
   <LI>Mult. SNPs(138) - SNPs mapping in more than one place on reference assembly.</LI>
   <LI>All SNPs(138) - all SNPs from dbSNP mapping to reference assembly.</LI>
 
 </UL>
 
 <H2>Interpreting and Configuring the Graphical Display</H2>
 <P>
   Variants are shown as single tick marks at most zoom levels.
   When viewing the track at or near base-level resolution, the displayed
   width of the SNP corresponds to the width of the variant in the reference
   sequence. Insertions are indicated by a single tick mark displayed between
@@ -416,32 +416,33 @@
       SNPAlleleFreq_TGP.bcp.gz .</LI>
   <LI>Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and 
       SNPSubSNPLink.bcp.gz.</LI>
   <LI>SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,
        such as clinically-associated.  See the document 
        <A HREF="ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_v5.pdf"
         target="_blank">dbSNP_BitField_v5.pdf</A> for details.</LI>
   <LI>The header lines in the rs_fasta files were used for molecule type,
       class and observed polymorphism.</LI>
   </UL>
 
 <H2>Data Access</H2>
 <P>
 The raw data can be explored interactively with the <A HREF="../../cgi-bin/hgTables"TARGET=_blank>Table Browser</a>,
 <A HREF="../../cgi-bin/hgIntegrator"TARGET=_blank>Data Integrator</a>, or <A HREF="../../cgi-bin/hgVai"TARGET=_blank>Variant Annotation Integrator</a>.
-For automated analysis, the genome annotation can be downloaded from the downloads server for <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/"TARGET=_blank>mm10</a>,
-<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/susScr3/database/"TARGET=_blank>susScr3</a>, <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/"TARGET=_blank>hg19</a>, 
+For automated analysis, the genome annotation can be downloaded from the downloads server for  <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/">hg38</a>, 
+ <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/">hg19</a>, <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/"TARGET=_blank>mm10</a>,
+<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/susScr3/database/"TARGET=_blank>susScr3</a>, 
 <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/bosTau7/database/"TARGET=_blank>bosTau7</a>, and <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/galGal4/database/"TARGET=_blank>galGal4</a> 
 (snp138*.txt.gz) or the <A HREF="../goldenPath/help/mysql.html"TARGET=_blank>public MySQL server</a>.
 Please refer to our <A HREF="https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!search/download+snps"TARGET=_blank>mailing list archives</a>
 for questions and example queries, or our <A HREF="../FAQ/FAQdownloads.html#download36"TARGET=_blank>Data Access FAQ</a> for more information.
 
 
 </P>
 
 <H2>Orthologous Alleles (human assemblies only)</H2>
 <P>
 For the human assembly, we provide a related table that contains
 orthologous alleles in the chimpanzee, orangutan and rhesus macaque
 reference genome assemblies.  
 We use our liftOver utility to identify the orthologous alleles.  
 The candidate human SNPs are a filtered list that meet the criteria: