90aae127020bbc1565bb62626d030cfac2bd83b4
rhead
  Mon Apr 18 16:14:11 2011 -0700
On SNP 132 description, changed single -> multiple, and standardized punctuation on PAR.
diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index 108a12f..70a8ca5 100644
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -1,176 +1,176 @@
 <!--News Section----------------------------------------------->  
         <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1">
             <TR><TD>        
             <TABLE BGCOLOR="#fffee8" WIDTH="100%"  BORDER="0" CELLSPACING="0" CELLPADDING="0">
                 <TR><TD>        
                 <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0>
                     <TR><TD>
                     <!--cheap trick to get background on row to be continuous-->
                     <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%">
                         <TR><TD ALIGN="left">
                           <FONT SIZE="4"><A NAME="TOC"></A><B>&nbsp; News</B></FONT></TD>
                         <TD ALIGN="right"><A HREF="goldenPath/newsarch.html"><IMG 
                         SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A>
                     </TD></TR></TABLE>
                 </TD></TR></TABLE>
                 <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0>
                     <TR><TH HEIGHT=3></TH></TR>
                     <TR><TD WIDTH=10></TD>
                     <TD>
                     <P>
                     To receive announcements of new genome 
                     assembly releases, new software features, updates and 
                     training seminars by email, subscribe to the
                     <A HREF="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" 
                     TARGET=_blank>genome-announce</A> mailing list.</P>
 
             
             <!-- start news -->
 
             <!-- hg19 snp132 release -->
 		    <P>
                     <FONT FACE="courier" SIZE="3"><B>18 April 2011 - dbSNP 132 Available for hg19</B></FONT>
 		    </P>
                     <P>
                     We are pleased to announce the release of four tracks derived from
                     <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" target=_blank>dbSNP</a>
                     build 132, available on the human assembly (GRCh37/hg19).
                     dbSNP build 132 is available at NCBI. The new tracks contain
                     additional annotation data not included in previous dbSNP tracks, 
                     with corresponding coloring and filtering options in the Genome
                     Browser.
                     </P>
                     <P>
                     As for prior builds of dbSNP, there is a track that contains all
                     mappings of reference SNPs to the human assembly; it is now labeled
                     &quot;All SNPs (132)&quot;.  Three new tracks have been added to show
                     interesting and easily defined subsets of dbSNP:
                     </P>
                     <ul>
                     <li> Common SNPs (132): uniquely mapped variants that appear in at
                     least 1% of the population</li>
 
                     <li>Flagged SNPs (132): uniquely mapped variants, excluding Common
                     SNPs, that have been flagged by dbSNP as &quot;clinically associated&quot;</li>
 
                     <li>Mult. SNPs (132): variants that have been mapped to more than one
                     genomic location</li>
                     </ul>
                     <P>
                     By default, only the Common SNPs (132) are visible; other tracks must
                     be made visible using the track controls.
                     </P>
                     <P>
                     The counts of distinct reference SNPs and their mappings to hg19
                     differ greatly among the tracks:
                     </P>
                     <table border="1" cellpadding="3">
                       <tr>
                         <th>Track</th>
                         <th>Reference SNPs</th>
                         <th>Mappings to hg19</th>
                       </tr>
                       <tr>
                         <td>Common SNPs (132)</td>
                         <td>13,842,381</td>
                         <td>14,024,295 *</td>
                       </tr>
                       <tr>
                         <td>Flagged SNPs (132)</td>
                         <td>17,899</td>
                         <td>18,084 *</td>
                       </tr>
                       <tr>
                         <td>Mult. SNPs (132)</td>
                         <td>1,114,599</td>
                         <td>3,568,988</td>
                       </tr>
                       <tr>
                         <td>All SNPs (132)</td>
                         <td>30,030,754</td>
                         <td>33,026,121</td>
                       </tr>
                     </table>
                     <P>
-                    * There are more mappings than SNPs even for the Common and Flagged
-                    subsets, because single mappings to alternate haplotype sequences
-                    and the Pseudo-Autosomal Regions on X and Y don't disqualify a SNP
+                    * There are more mappings than SNPs for the Common and Flagged
+                    subsets because multiple mappings to alternate haplotype sequences
+                    or the pseudoautosomal regions on X and Y don't disqualify a SNP
                     from consideration as uniquely mapped.
 		    </P>
                     <P>
                     You will find the four SNPs (132) tracks on the Human Feb. 2009
                     (GRCh37/hg19) browser in the &quot;Variation and Repeats&quot; group.
 		    </P>
                     <P>
                     Many thanks to dbSNP at NCBI for the data, and to 
                     <a href="http://www.gs.washington.edu/faculty/king.htm"
                        target=_blank>Mary-Claire King</a>                    
                     at the University of Washington for helpful comments that motivated
                     us to enhance our dbSNP annotations. The tracks were produced at UCSC
                     by Angie Hinrichs, Brooke Rhead, Bob Kuhn, and Jim Kent.
 		    </P>
 
                     <HR>  
             
             <!-- SHEEP BROWSER RELEASE -->
 		    <p>
              <font face="courier" size="3"><b>18 April 2011 - Sheep Browser Released</b></font>
 		    </p>
 		    
 		    <p>We are happy to announce a Genome Browser for
 		    the initial release of sheep (<em>Ovis aries</em>) genome. The Feb. 2010 <em>Ovis
 			aries</em> draft assembly (NCBI project <a
 			href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10709"
 			target=_blank>10709</a>, <a
 			href="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Ovis_aries/
 			Ovis_aries_1.0/" target=_blank>GCA_000005525.1</a>) was produced by the <a
 			href="http://www.sheephapmap.org/" target=_blank>International Sheep Genomics Consortium (ISGC)
 			sequencing center</a>. The mitochondrial genome was sequenced by <a href="http://www.uni-giessen.de/cms/"
 			target=_blank>Justus-Liebig-University</a>.</p>
 		    
 		    <p>There are 27 chromosomes: chr1 - chr26, chrX, plus the mitochondrial sequence chrM from
 			genbank accession NC_001941, for a total sequence length of 2,860,512,983 bases. There are
 			1,659,241,706 'N' bases in gaps, leaving 1,201,271,277 ACGT bases.</p>
 			
 			<p>The genome has been sequenced using 454 FLX sequencing to 3X coverage (DNA derived from
 			six female sheep each sequenced with 0.5X coverage). Contigs were assembled based on alignment to
 			the bovine genome and ordered into ovine chromosomes using BAC-end sequences and the virtual sheep
 			genome.</p>
 			
 			<p>We'd like to thank the International Sheep Genomics Consortium (ISGC)
 			sequencing center and Justus-Liebig-University for providing this assembly.
 		    We'd also like to acknowledge the UCSC team who worked on 
 		    this release: Chin Li, Greg Roe, and Luvina Guruvadoo. 
 		    The sheep browser annotation tracks were generated by 
 		    UCSC and collaborators worldwide.</p>
 
 		    <hr>
 
             <p><FONT FACE="courier" SIZE="3"><B>04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs: </B></FONT>
                     Consensus was reached on color standards to represent CNV loss (red) 
 		    and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA 
 		    during the 1st annual ISCA Scientific Conference.
 		    <A HREF="goldenPath/newsarch.html#030411">Read more</A>
 		    </p>
 		    
 		    <p><FONT FACE="courier" SIZE="3"><B>01 March 2011 - Updated Chimpanzee Browser Released: </B></FONT>
             We are happy to announce the release of a Genome Browser for
 		    the latest release of the chimpanzee (<em>Pan 
 		    troglodytes</em>) genome.
 		    <A HREF="goldenPath/newsarch.html#030111">Read more</A>
 		    </p>
                    
                    <p><FONT FACE="courier" SIZE="3"><B>19 January 2011 -
 Browser Released for Zebrafish Zv9 Assembly: </B></FONT>
                     The most recent zebrafish assembly -- Zv9 (UCSC version
                     danRer7, Jul. 2010) -- is now available in the UCSC
                     Genome Browser. 
 		    <A HREF="goldenPath/newsarch.html#011911">Read more</A>
 		    </p>
 
 ==> <a href="goldenPath/newsarch.html">News Archives</a>
 
                     </TD><TD WIDTH=15>
                  </TD></TR></TABLE>
             <BR></TD></TR></TABLE>
         </TD></TR></TABLE>
