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<H1>[dbsnp-announce] RELEASE: NCBI dbSNP Build 137 for Human</H1>
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<B>Public announcements regarding dbSNP</B>
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<A HREF="mailto:dbsnp-announce%40ncbi.nlm.nih.gov?Subject=Re%3A%20%5Bdbsnp-announce%5D%20RELEASE%3A%20NCBI%20dbSNP%20Build%20137%20for%20Human&In-Reply-To=%3Cmailman.38770.1340759599.20059.dbsnp-announce%40ncbi.nlm.nih.gov%3E"
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TITLE="[dbsnp-announce] RELEASE: NCBI dbSNP Build 137 for Human">dbsnp-announce at ncbi.nlm.nih.gov
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</A><BR>
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<I>Tue Jun 26 21:13:16 EDT 2012</I>
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<PRE>RELEASE: NCBI dbSNP Build 137 for Human
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dbSNP Build 137 for Human (txid 9606)
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===================================
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This dbSNP build is based on Genome Reference Consortium (GRC) assembly GRCh37.p5, which is a patch release of GRCh37 that includes minor changes that are described in the README for this patch release: <A HREF="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p5/.">ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p5/.</A>
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dbSNP build 137 includes new submissions from the 1000 Genomes Project phase I release (dbSNP Handle: 1000Genomes) and from the ClinSeq Sequencing Project (dbSNP handle: CLINSEQ-SNP). Listed below are the number of submitted SNPs (ss) and assigned Reference SNP (rs) clusters that are in B137 for these two submitters:
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dbSNP Handle ss_cnt rs_cnt
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------------------- -------- --------
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1000GENOMES 2157571 2156169
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CLINSEQ_SNP 374499 374497
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Build Summary
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-------------------
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organism: Homo sapiens
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tax_id: 9606
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total_ss: 187,852,828
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total_rs: 53,558,214
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new_ss(since b135 release on Oct 13, 2011): 9,572,078
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new_rs(since b135 release on Oct 13, 2011): 2,708,655
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Component Availability Dates
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--------------------------------------
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Component Date Available
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dbSNP web query June 26, 2012
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FTP data June 26, 2012
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Entrez Search June 26, 2012
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**Please note that there is a slight discrepancy in the GMAF for B137 as well as in the MAF for two populations in B137 due to the presence of non-founder individuals in the populations used in the calculations. The effect of the non-founders on the calculations was minimal:
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Population Total Size Extra Samples Discrepancy
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Global 1092 3 0.27%
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MXL 66 2 4.54%
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LWK 97 1 1.03%
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In the interest of expediency we released the data since the discrepancies were small, and will release a corrected version of the data at a future date.
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* All formats and conventions for this build are described in ftp.ncbi.nih.gov/snp/00readme.txt. Please note that we update this README document only on a periodic basis.
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* Complete data for build 137 will be available in multiple formats, and are separated by organism. The data are available at <A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/">ftp://ftp.ncbi.nih.gov/snp/organisms/</A>
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* The complete build summary for build 137 is available at:www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi
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Updates and New Features for SNP Build 137
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A. New BED FTP dump
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dbSNP now provides data in dbSNP BED files. The data in these files are separated by chromosome and are available at: <A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/BED.">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/BED.</A>
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To see a general description of the BED file format and how it is used, see <A HREF="http://users.soe.ucsc.edu/~kent/gbd.html#BED">http://users.soe.ucsc.edu/~kent/gbd.html#BED</A>
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The BED contents were derived from dbSNP RS Docsum ASN.1 (<A HREF="ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.3.xsd">ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.3.xsd</A>). BED column descriptions and mapping to ASN.1 fields are described at <A HREF="ftp://ftp.ncbi.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt.">ftp://ftp.ncbi.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt.</A>
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B. Indel Clustering Adjustment
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During the creation of B137, single base indel variations that collocated in a homopolymer stretch were merged into a single refSNP (rs) number. The resulting position of each merged indel refSNP was adjusted to start at the first base of the repeating nucleotide nearest the beginning of the homopolymer sequence. A total of 2,617,241 indel refSNPs were merged, giving a final total of 1,203,487 indel refSNPs
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Merge histories for indel refSNPs are located at:
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/indel_clustering_fix.README">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/indel_clustering_fix.README</A> <A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/indel_clustering_fix.txt.gz">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/indel_clustering_fix.txt.gz</A>
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C. Variation Reporter Perl API
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NCBI Variation Group has released a Perl module Variation:Reporter that will allow you to programmatically access the NCBI Variation Reporter service (<A HREF="http://www.ncbi.nlm.nih.gov/variation/tools/reporter/docs/help">http://www.ncbi.nlm.nih.gov/variation/tools/reporter/docs/help</A>). The module can be downloaded from NCBI at <A HREF="ftp://ftp.ncbi.nih.gov/variation/tools/API/Variation.zip">ftp://ftp.ncbi.nih.gov/variation/tools/API/Variation.zip</A> .
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Instructions for using and installing the module are located in the README that comes in the module download.
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D. Entrez SNP has a New Look
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The Entrez SNP web site (<A HREF="http://www.ncbi.nlm.nih.gov/snp">http://www.ncbi.nlm.nih.gov/snp</A>) is now live and has a new look and user interface similar to other NCBI resources to provide a more consistent user experience. Except for the new look and the removal of some reports (see NOTE below) which are more appropriate as downloads than web display, the search functions and reporting will remain the same for now. Gradually over the next year additional changes will be made to improve search functions and variation reporting.
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NOTE: The following infrequently viewed reports have been removed from the Entrez web display:
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XML
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ASN.1
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UID list (uilist)
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Submitted SS exemplar (ssexemplar)
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Merge Status (mergestatus)
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Genotype xml (genxml)
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Frequency xml (freqxml)
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RefSNP Cluster Report (RSR) - Abbreviated version
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Although the above reports will no longer be available as selected web display options, you can still access them using any of the following channels:
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1. Entrez Web Search: Use the download option. See <A HREF="http://dev.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Displaying_and_Saving_a_Set_o">http://dev.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Displaying_and_Saving_a_Set_o</A> afor instructions on how to use the download option.
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2. Entrez eUtils: <A HREF="http://dev.ncbi.nlm.nih.gov/books/NBK25501/">http://dev.ncbi.nlm.nih.gov/books/NBK25501/</A>
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3. dbSNP build FTP dumps: <A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/</A>
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4. dbSNP batch query service: <A HREF="http://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html">http://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html</A>
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Contact <A HREF="http://www.ncbi.nlm.nih.gov/mailman/listinfo/dbsnp-announce">snp-admin at ncbi.nlm.ncbi.nih.gov</A> if you have any questions or concerns regarding this change.
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dbSNP Production Team
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June 26, 2012
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National Center for Biotechnology Information (NCBI)
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National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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</PRE>
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