aea06327a4095872b6078777e50859e63b064a2c
lrnassar
  Thu Aug 1 13:21:27 2019 -0700
Updating NCBI UCSC comparison of FAQrelease #23611

diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html
index be41d4c..e117515 100755
--- src/hg/htdocs/FAQ/FAQreleases.html
+++ src/hg/htdocs/FAQ/FAQreleases.html
@@ -318,33 +318,35 @@
 at other sites. Each track has an associated description page that credits the authors of the 
 annotation.</p> 
 <p>
 For detailed information about the individuals and organizations who contributed to a specific 
 assembly, see the <a href="../goldenPath/credits.html">Credits</a> page.</p>
 
 <a name="release4"></a>
 <h2>Comparison of UCSC and NCBI human assemblies</h2>
 <h6>How do the human assemblies displayed in the UCSC Genome Browser differ from the NCBI human 
 assemblies?</h6>
 <p> 
 Human assemblies displayed in the Genome Browser (hg10 and higher) are near identical to the 
 NCBI assemblies when it comes to primary sequence. Minor differences may be present, however.
 Sources include:</p>
 <ul>
-  <li>We repeat mask our own genomes</li>
-  <li>All UCSC chroms use the 'chr1' nomenclature, whereas certain NCBI schemas may only 
-      have the numbers (chr1 = 1)</li>
+  <li>NCBI genomes are repeat masked with RepeatMasker, however, UCSC genomes are independently 
+      masked with both RepeatMasker (with different flags) and WindowMasker, ultimately using 
+      the program output with the highest percentage masked for the base sequence</li>
+  <li>In genome download files, UCSC uses the 'chr1' nomenclature for sequence identifiers, 
+      whereas the primary NCBI sequence identifiers are RefSeq accessions</li>
   <li>The mitochondrion for hg19 differs from the one in NCBI (GRCh37)</li>
 </ul>
 
 <a name="release12"></a>
 <h2>Differences between UCSC and NCBI mouse assemblies</h2>
 <h6>Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the
 NCBI website?</h6>
 <p> 
 The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI 
 web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). 
 NCBI provides data for several additional strains in their builds.</p>
 
 <a name="release5"></a>
 <h2>Accessing older assembly versions</h2>
 <h6>I need to access an older version of a genome assembly that's no longer listed in the Genome