This track displays common structural variants (SVs) from nstd186 (NCBI Curated Common Structural Variants), divided into subtracks by source study and by population.
nstd186 is a curated collection of structural variants in dbVar from studies with at least 100 samples, that include allele frequency data, and that have an allele frequency of >=0.01 in at least one population. It includes copy number gains and losses, copy number variations, duplications, deletions, insertions, and mobile element variants (ALU, LINE1, SVA, HERV).
The dataset aggregates variants from six source studies:
For the latest nstd186 variant call counts and version history, see the nstd186 summary page at NCBI.
Per-source-study subtracks (variants from nstd186 attributed to one of the six component studies):
Per-population subtracks (variants with AF >= 0.01 aggregated across nstd186 source studies for each super-population):
The NCBI dbVar Track Hub additionally provides population-only variants (variants common in one population but not in any other): African only, American only, East Asian only, European only, and South Asian only. These are not loaded as native Genome Browser tracks; connect to the hub to view them.
Items in all subtracks follow the same conventions. Variants are colored by type, using the dbVar color scheme described in the dbVar Overview page:
| Color | Variant Type(s) |
|---|---|
| copy number loss, deletion (including mobile element deletions) | |
| copy number gain, duplication, insertion (including mobile element insertions) | |
| copy number variation |
Mouseover on items shows genes affected, size, variant type, allele count (AC), allele number (AN), allele frequency (AF), and population (in per-population subtracks).
Subtracks can be filtered by:
The Hide empty subtracks option on the track configuration page hides subtracks that have no data in the current viewing window. This is enabled by default and can be toggled off.
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 at the dbVar nstd186 data access page, or in the dbVar Track Hub. For questions about dbVar track data, please contact dbvar@ncbi.nlm.nih.gov.
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.
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