Description
This track displays common copy number genomic variations from nstd186 (NCBI Curated Common
Structural Variants), divided into subtracks according to population and source of original
submission.
This curated dataset of all structural variants in dbVar includes variants from gnomAD, 1000
Genomes Phase 3, and DECIPHER (dbVar studies
nstd166,
estd219, and
nstd183, respectively).
It only includes copy number gain, copy number loss, copy number variation, duplications, and
deletions (including mobile element deletions), that are part of a study with at least 100 samples,
include allele frequency data, and have an allele frequency of >=0.01 in at least one population.
For more information on the number of variant calls and latest statistics for nstd186 see
Summary of nstd186
(NCBI Curated Common Structural Variants).
There are six subtracks in this track set:
- NCBI Curated Common SVs: African -
Variants with AF >= 0.01 for
African Population.
- NCBI Curated Common SVs: European -
Variants with AF >= 0.01 for
European Population.
- NCBI Curated Common SVs: all populations -
Variants with AF >= 0.01 for
Global Population.
- NCBI Curated Common SVs: all populations from gnomAD -
Variants with AF >= 0.01 from
gnomAD Structural Variants.
- NCBI Curated Common SVs: all populations from 1000 Genomes -
Variants with AF >= 0.01 from
1000 Genomes Consortium Phase 3 Integrated SV.
- NCBI Curated Common SVs: all populations from DECIPHER -
Variants with AF >= 0.01 from
DECIPHER Consensus CNVs.
Display Conventions and Configuration
Items in all subtracks follow the same conventions: items are colored by variant type, and are
based on the dbVar colors described in the
dbVar Overview page.
Red for copy number loss or deletion,
blue for copy number gain or duplication, and
violet for copy number variation.
Mouseover on items indicates genes affected, size, variant type, and allele frequencies (AF).
All tracks can be filtered according to the Variant Size and Variant Type.
Data Access
The raw data can be explored interactively with the
Table Browser, or the
Data Integrator. For automated analysis,
the data may be queried from our
REST API.
The data can also be found directly from the dbVar
nstd186 data access, as well as in the
dbVar Track Hub, where additional subtracks are included. For questions about
dbVar track data, please contact
dbvar@ncbi.nlm.nih.gov
.
Credits
Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical
coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter, of
the Genome Browser team for engineering the track display.
References
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M,
Zhou G et al.
DbVar and DGVa: public archives for genomic structural variation.
Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41.
PMID: 23193291; PMC: PMC3531204
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