Description

The tracks listed here contain data from the nstd186 (NCBI Curated Common Structural Variants) study. This is a collection of structural variants (SV) originally submitted to dbVar which are part of a study with at least 100 samples and have an allele frequency of >=0.01 in at least one population. The complete dataset is imported from these common-population studies:

gnomAD Structural Variants (nstd166): Catalog of SVs detected from the sequencing of the complete genome of 10,847 unrelated individuals from the GnomAD v2.1 release.

1000 Genomes Consortium Phase 3 Integrated SV (estd219): Structural variants of the 1000 Genomes project Phase 3 as reported in a separate article specifically dedicated to the analysis of SVs. Many of these data are identical to those reported in the estd214 study.

DECIPHER Common CNVs (nstd183): Consensus set of common population CNVs selected from high-resolution controls sets where frequency information is available.

There are two tracks in this collection:

• NCBI dbVar Curated Common Structural Variants (dbVar Common SV): Shows copy number variants calls (variants >=50 nucleotides) from the nstd186 study.
• NCBI dbVar Curated Conflict Variants (dbVar Conflict SV): Shows copy number variants from nstd186 (NCBI Curated Common Structural Variants) that overlap with nstd102 (Clinical Structural Variants).

Display Conventions

These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Some dbVar tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page.

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