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NCBI Curated Common Structural Variants

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 Configure 		 NCBI Curated Common SVs in African Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in All populations  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in All populations from 1000 Genomes  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in All populations from Abel  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in All populations from Byrska-Bishop  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in All populations from DECIPHER  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in All populations from gnomAD  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in All populations from Lee  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in American Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in East Asian Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in European Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in Other Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs in South Asian Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs Only in African Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs Only in American Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs Only in East Asian Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs Only in European Population  NCBI Curated Common Structural Variants   Data format 
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 Configure 		 NCBI Curated Common SVs Only in South Asian Population  NCBI Curated Common Structural Variants   Data format 
    
Assembly: Human Feb. 2009 (GRCh37/hg19)

Description

Variants from the dbVar study nstd186 (NCBI Curated Common Structural Variants), which is a curated collection of structural variants from studies with at least 100 samples, include allele frequency data, and have an allele frequency of >=0.01 in at least one population. Separate subtracks allow distinction between different populations and original data sources. Allele frequencies are aggregated on these super-populations: global, African, American, East Asian, European, South Asian, other. This track includes copy number variations, gains, duplications, insertions, losses, and deletions. For questions about dbVar track data, please contact dbvar.

Data Updates

nstd186 (NCBI Curated Common Structural Variants) combines data from multiple studies in dbVar. A detailed summary and history of nstd186 can be found in the summary page of Common variants in dbVar.

This track contains data from the following studies:

Subtracks

The NCBI Curated Common Structural variants are separated into subtracks according to population and data source:

Non-Redundant

Except for the _Only_ subtracks, this track is non-redundant with respect to placement and variant type. The label contains the values of the variant with the highest allele frequency at the placement and variant type.

Display Conventions and Configuration

Labels

The variant label is the dbVar variant call accession (nssv).

Mouseover

The mouseover (displayed when the mouse is hovered over a variant) shows the following:

  • List of Affected Genes
  • Position
  • Size
  • Variant Type
  • Allele Count
  • Allele Number
  • Allele Frequency
  • Population (if population-specific track)
  • Total number of redundant calls

Detail Page

The detail page contains the following:

Variant Colors

The colors indicate variant type, and are based on the dbVar colors described in the dbVar Overview page.

Placements

For simplicity, the BED files and tracks only contain the variants' outer-most start and stop placements. The actual variant placements may consist of exact start/stop with breakpoint resolution, inner-placements only, outer-placements-only, or some combination. For full details of variant placements, follow the links to the variant pages in dbVar.

Filters

The tracks can be filtered by the following:

  • Frequency Range
  • Variant Length Range
  • Variant Type

Statistics

Counts per subtrack for each filter value:

Frequency Range

Value common_1000g common_abel common_african common_american common_byrska_bishop common_decipher common_east_asian common_european common_global common_gnomad common_lee common_other common_south_asian
0.02 to 0.05 3071 2742 7976 4469 5482 5079 2602 4235 19671 5220 53 4592 1641
0.05 to 0.1 1954 2110 7269 3865 3616 3401 3154 4011 12904 2913 56 2554 1569
0.1 to 0.2 1927 2582 7195 5457 3972 1558 4505 5393 13847 4855 80 4334 1733
0.2 to 0.5 2664 3802 8589 7762 6086 1326 7737 7682 18103 5520 237 5480 2719
Over 0.5 1112 2158 3711 3836 4195 864 4288 3875 10819 2464 655 2550 1212
Under 0.02 3101 2005 1706 3759 5289 3667 1399 1622 17498 5369 22 3524 846
Total 13829 15399 36446 29148 28640 15895 23685 26818 92842 26341 1103 23034 9720

Variant Length Range

Value common_1000g common_abel common_african common_american common_byrska_bishop common_decipher common_east_asian common_european common_global common_gnomad common_lee common_other common_south_asian
100KB to 1MB 89 78 190 191 291 476 178 162 1059 131 0 109 72
10KB to 100KB 1076 495 2509 2330 1754 1914 2090 2225 6775 1747 0 1566 766
Over 1MB 0 1 2 1 11 46 2 1 60 2 0 2 0
Under 10KB 12664 14825 33745 26626 26584 13459 21415 24430 84948 24461 1103 21357 8882
Total 13829 15399 36446 29148 28640 15895 23685 26818 92842 26341 1103 23034 9720

Variant Type

Value common_1000g common_abel common_african common_american common_byrska_bishop common_decipher common_east_asian common_european common_global common_gnomad common_lee common_other common_south_asian
alu deletion 1094 2114 1078 1037 0 0 957 990 3207 0 0 0 1007
alu insertion 4490 0 5650 4302 4845 0 3456 3914 11106 2044 0 1580 3052
copy number gain 305 0 262 255 0 0 221 218 305 0 0 0 241
copy number loss 335 0 285 266 0 0 197 222 335 0 0 0 234
copy number variation 511 0 1553 1535 325 0 1397 1483 1944 1108 0 1055 393
deletion 6061 10072 16788 13519 14012 13974 10828 12419 49888 12523 0 11020 4088
duplication 84 2775 2222 1652 4595 1921 1355 1563 11002 2420 0 2009 41
herv deletion 1 0 1 1 0 0 0 1 1 0 0 0 0
insertion 27 0 7281 5521 4081 0 4421 5072 12292 7589 1103 6837 14
line1 deletion 53 331 53 51 0 0 48 49 383 0 0 0 48
line1 insertion 591 0 830 657 440 0 528 567 1416 410 0 329 399
mobile element deletion 0 0 0 0 43 0 0 0 43 0 0 0 0
mobile element insertion 0 0 34 21 19 0 18 21 56 38 0 33 0
sva deletion 8 107 8 7 0 0 7 7 115 0 0 0 7
sva insertion 269 0 401 324 280 0 252 292 749 209 0 171 196
Total 13829 15399 36446 29148 28640 15895 23685 26818 92842 26341 1103 23034 9720

Data Access

Data for this track can be downloaded from the following locations:

Methods

Generating the NCBI Curated Common Structural Variant Tracks consists of the following:

References