Tag: RefSNP

Non-human variation data from EVA now available in the Genome Data Viewer

You can now view SNP variation data for many commonly studied animals and plants – including mouse, cow, Drosophila, Arabidopsis, maize, cabbage, and many more – in the Genome Data Viewer (GDV) and other graphical sequence viewers. This data is streamed from the European Variation Archive (EVA) at the European Bioinformatics Institute (EBI).

On any NCBI graphical sequence view you can use the Configure Tracks menu and the Track Configuration Panel to add the track for the EVA RefSNP data. This track is available through the left-hand tab for Remote Variation Data (Figure 1). The EVA RefSNP track displayed on the pig (Sus scrofa) chromosome 12 graphical view is shown in Figure 2.

Config_tracks Figure 1. The Track Configuration panel showing the Remote Variation Data tab and he EVA RefSNP Release 1 track. Select the track checkbox and click Configure to load the track.

pig_snps Figure 2. The graphical sequence viewer showing the region of the growth hormone gene on pig chromosome 12 (NC_010454.4) with the EVA RefSNP Release 1 track at the bottom. The track header has an (R) and a green highlight to indicate that it is remote data streamed from an external website. NCBI is not responsible for the content or availability of these data.

The EVA SNP FTP site has more information about the EVA SNP data release.

Please contact us using the Feedback link on the graphical view to let us know what you think and how we can further improve your experience with the NCBI genome browsers and graphical sequence viewers

dbSNP human build 154 release + ALFA data

dbSNP human build 154, now available, includes new ALFA (Allele Frequency Aggregator) variants and allele frequency. This build contains over two billion Submitted SNP (ss) records and 730 million Reference SNP (rs) records.

New features include:

dbSNP search now support HGVS and protein variant search
RefSNP page linked to Litvar information
Filter and facet to retrieve all SNPs with ALFA frequency

See the release notes for more information about what’s new in build 154.

April 22 Webinar on NCBI’s ALFA: allele frequency data for variant analysis and interpretation

On Wednesday, April 22, 2020 at 12 PM, join NCBI staff to learn how results from the Allele Frequency Aggregator (ALFA) project will help you interpret the biological impact of common and rare sequence variants. ALFA’s initial release includes analysis of genotype data from ~100K unrestricted dbGaP subjects and provides high-quality allele frequency data now displayed on relevant dbSNP records. In this webinar, you will learn about the data in the recent ALFA release, see how to access the data from the web, FTP, and how to programmatically retrieve data by positions, genes, and other attributes using E-utilities and Variation Services API in Python.

Date and time: Wed, Apr 22, 2020 12:00 PM – 12:45 PM EDT
Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

dbSNP celebrates 20 years!

dbSNP was established in August 1999 as a collaboration between NCBI and the National Human Genome Research Institute (NHGRI) as a database of small scale nucleotide variants. The database includes both common and rare single-base nucleotide variation (SNV), short (=< 50bp) deletion/insertion polymorphisms, and other classes of small genetic variations.

Continue reading “dbSNP celebrates 20 years!” →

NCBI releases newly designed dbSNP RefSNP Report – Alpha version

NCBI dbSNP is pleased to announce a newly designed Reference SNP (RefSNP, rs) Report webpage to provide enhanced performance and presentation for access to individual RefSNP records. This Alpha version of the report enables browsing of submitted and computed RefSNP variant data from the redesigned dbSNP build system.

The new RefSNP report (alpha version). You can see all of the sections described in the blog post, like the summary section and the sidebar menu. — **Figure 1.** The dbSNP RefSNP Report Alpha for rs268.

Continue reading “NCBI releases newly designed dbSNP RefSNP Report – Alpha version” →

dbSNP’s human build 150 has doubled the amount of RefSNP records!

dbSNP’s Human Build 150 includes a large number of new submissions from the Human Longevity, Inc. (HLI) and TopMed, increasing the total number of Human RefSNPs in the database from 154 to 324 million. TopMed has also provided new allele frequency data for 163 million RefSNPs.

Continue reading “dbSNP’s human build 150 has doubled the amount of RefSNP records!” →