493b876f63894c017c1659b03a896324749a809e rhead Mon Apr 18 16:51:40 2011 -0700 On the snp132 announcement, tried to make the sentence about multiple mappings more readable and informative... thanks, Mark. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 70a8ca5..19d84d2 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,176 +1,179 @@
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18 April 2011 - dbSNP 132 Available for hg19

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 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.

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:

  • Common SNPs (132): uniquely mapped variants that appear in at least 1% of the population
  • Flagged SNPs (132): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated"
  • Mult. SNPs (132): variants that have been mapped to more than one genomic location

By default, only the Common SNPs (132) are visible; other tracks must be made visible using the track controls.

The counts of distinct reference SNPs and their mappings to hg19 differ greatly among the tracks:

Track Reference SNPs Mappings to hg19
Common SNPs (132) 13,842,381 14,024,295 *
Flagged SNPs (132) 17,899 18,084 *
Mult. SNPs (132) 1,114,599 3,568,988
All SNPs (132) 30,030,754 33,026,121

- * 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. + + * The Common and Flagged tracks have more mappings than SNPs due to the + alternate haplotype sequences and the pseudoautosomal regions on X and Y. + SNPs are considered uniquely mapped if they map only once to a haploid + reference genome. These regions add non-haploid sequence to the reference + genome; therefore, multiple mappings involving these regions are still + considered unique.

You will find the four SNPs (132) tracks on the Human Feb. 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group.

Many thanks to dbSNP at NCBI for the data, and to Mary-Claire King 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.

18 April 2011 - Sheep Browser Released

We are happy to announce a Genome Browser for the initial release of sheep (Ovis aries) genome. The Feb. 2010 Ovis aries draft assembly (NCBI project 10709, GCA_000005525.1) was produced by the International Sheep Genomics Consortium (ISGC) sequencing center. The mitochondrial genome was sequenced by Justus-Liebig-University.

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.

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.

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.

04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs: 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. Read more

01 March 2011 - Updated Chimpanzee Browser Released: We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan troglodytes) genome. Read more

19 January 2011 - Browser Released for Zebrafish Zv9 Assembly: The most recent zebrafish assembly -- Zv9 (UCSC version danRer7, Jul. 2010) -- is now available in the UCSC Genome Browser. Read more

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