c587d5eb02bb241e36ddead11497ce2426c0c7d4 rhead Mon Apr 18 13:43:11 2011 -0700 Added snp132 announcement. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 628d5d8..90d2126 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -15,30 +15,115 @@ </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 March 2011 - dbSNP 132 Available for hg19</B></FONT> + </P> + <P> + We are pleased to announce the release of four tracks derived from + dbSNP build 132, available on the human assembly (GRCh37/hg19). + dbSNP build 132 is <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" + target=_blank>available at NCBI</a>. 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 + "All SNPs (132)". 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 "clinically associated"</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 + 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 "Variation and Repeats" 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 style="font-weight: bold; font-size: 16px; font-family: 'courier', serif"> 18 March 2011 - Sheep Browser Released </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>