Schema for dbVar Common SV - NCBI dbVar Curated Common Structural Variants
  Database: hg38    Primary Table: dbVar_common_global Data last updated: 2020-09-22
Big Bed File Download: /gbdb/hg38/bbi/dbVar/common_global.bb
Item Count: 39,311
The data is stored in the binary BigBed format.

Format description: dbVar data with color plus Variant Type, Variant Length Range, and Frequency
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166077896Start position of feature on chromosome
chromEnd166077949End position of feature on chromosome
namenssv16168600dbVar Variant Accession
score1000Score
strand.+ or - for strand
thickStart166077896Start position of feature on chromosome
thickEnd166077949End position of feature on chromosome
reserved255,0,0Colors indicate Variant Type and Clinical Significance.
frequencyALL_AF=0.253566Allele Frequency (in population-specific tracks, this is the AF for that population)
typedeletionVariant Type
lengthUnder 10KBVariant Length Range
labelGene(s) affected: ,TMCO1, Position: chr1:166077897-166077949, Size: 53, Type: DEL, Allele Count: 5227, Allele Number: 20614, Allele Frequency: 0.253566Gene, Position, Size, Type, AC, AN, AF, Population (if not global), Total calls (if multiple calls with same position+type)
freq_range0.2 to 0.5Allele Frequency range
call_listList of dbVar Variant calls with the same placement and call type

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedfrequencytypelengthlabelfreq_rangecall_list
chr1166077896166077949nssv161686001000.166077896166077949255,0,0ALL_AF=0.253566deletionUnder 10KBGene(s) affected: ,TMCO1, Position: chr1:166077897-166077949, Size: 53, Type: DEL, Allele Count: 5227, Allele Number: 20614, All ...0.2 to 0.5
chr1166109829166109898nssv161799001000.166109829166109898255,0,0ALL_AF=0.03127deletionUnder 10KBGene(s) affected: FAM78B, Position: chr1:166109830-166109898, Size: 69, Type: DEL, Allele Count: 677, Allele Number: 21650, Alle ...0.02 to 0.05
chr1166210175166225426nssv161897471000.1662101751662254260,0,255ALL_AF=0.0297524copy number gain10KB to 100KBGene(s) affected: LOC112268276, Position: chr1:166210176-166225426, Size: 15251, Type: DUP, Allele Count: 149, Allele Number: 50 ...0.02 to 0.05
chr1166210175166225426nssv161908081000.16621017516622542679,28,115ALL_AF=0.0297524copy number variation10KB to 100KBGene(s) affected: LOC112268276, Position: chr1:166210176-166225426, Size: 15251, Type: MCNV, Allele Count: 149, Allele Number: 5 ...0.02 to 0.05
chr1166211989166226226nssv161679721000.1662119891662262260,0,255ALL_AF=0.056474duplication10KB to 100KBGene(s) affected: LOC112268276, Position: chr1:166211990-166226226, Size: 14237, Type: DUP, Allele Count: 1223, Allele Number: 2 ...0.05 to 0.1
chr1166240262166245763nssv161680081000.166240262166245763255,0,0ALL_AF=0.060654deletionUnder 10KBGene(s) affected: LOC112268276, Position: chr1:166240263-166245763, Size: 5501, Type: DEL, Allele Count: 1306, Allele Number: 21 ...0.05 to 0.1
chr1166304120166304273nssv161625111000.166304120166304273255,0,0ALL_AF=0.028116deletionUnder 10KBGene(s) affected: LOC112268276, Position: chr1:166304121-166304273, Size: 153, Type: DEL, Allele Count: 609, Allele Number: 2166 ...0.02 to 0.05
chr1166403448166410472nssv161856331000.166403448166410472255,0,0ALL_AF=0.013742072deletionUnder 10KBGene(s) affected: none, Position: chr1:166403449-166410472, Size: 7024, Type: DEL, Allele Count: 26, Allele Number: 1892, Allele ...Under 0.02
chr1166427343166428142nssv161646621000.166427343166428142255,0,0ALL_AF=0.011896deletionUnder 10KBGene(s) affected: none, Position: chr1:166427344-166428142, Size: 799, Type: DEL, Allele Count: 258, Allele Number: 21688, Allel ...Under 0.02
chr1166495295166502006nssv161861671000.166495295166502006255,0,0ALL_AF=0.013213531deletionUnder 10KBGene(s) affected: none, Position: chr1:166495296-166502006, Size: 6711, Type: DEL, Allele Count: 25, Allele Number: 1892, Allele ...Under 0.02

dbVar Common SV (dbVar_common) Track Description
 

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