Presumed Normal SV Track Settings
 
Presumed Normal Structural Variants in dbVar

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Variant Length Range Discovery Method Type Pathogenic Reciprocal Overlap Population Code Variant Type


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 Configure 		 Presumed Normal SVs  Presumed Normal Structural Variants in dbVar   Data format 
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 Configure 		 Structural Variants with Phenotype  Presumed Normal Structural Variants in dbVar   Data format 
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

Structural variants in dbVar excluding the following:

Data Updates

This track is updated with every dbVar monthly release.

Subtracks

The Presumed Normal Structural variants are separated into the following subtracks:

Non-Redundant

This track is non-redundant with respect to placement, variant type, and discovery method type. The label and detail fields contain the lists of unique values for each field of the redundant variant calls.

Display Conventions and Configuration

Labels

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

Mouseover

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

  • List of Affected Genes
  • Position
  • Size
  • Variant Type
  • dbVar study containing the variant
  • Discovery Method Type
  • List of unique phenotypes of the redundant calls (for phenotype subtrack)
  • List of unique populations derived from samples or samplesets of the redundant calls (if available)
  • Total number of redundant calls

Detail Page

The detail page contains the following:

Variant Colors

The colors indicate variant type of the variant, 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 track can be filtered by the following:

  • Variant Length Range
  • Discovery Method Type
  • Range of Reciprocal Overlap with Pathogenic Variant
  • Population Code derived from Sample or Sampleset
  • Variant Type

Statistics

Counts per subtrack for each filter value:

Variant Length Range

Value normal_healthy normal_phenotype
100KB to 1MB 208096 1185
10KB to 100KB 557575 2297
Over 1MB 40578 57
Under 10KB 4730303 7520
Total 5536552 11059

Discovery Method Type

Value normal_healthy normal_phenotype
Curated 42795 0
Merging 288817 395
Multiple 37855 0
Oligo aCGH 67504 80
Optical mapping 30497 1342
SNP array 371326 1759
Sequencing 4697676 7482
other 82 1
Total 5536552 11059

Range of Reciprocal Overlap with Pathogenic Variant

Value normal_healthy normal_phenotype
10 to 25 59702 302
25 to 50 31271 145
50 to 75 17084 173
75 to 90 7787 186
90 to 100 6719 150
none 5413989 10103
Total 5536552 11059

Population Code derived from Sample or Sampleset

Value normal_healthy normal_phenotype
AFR 45546 1
AMR 31245 0
EAS 16329 0
EUR 138967 67
OTH 3530 0
SAS 3771 0
mixed 19846 0
multiple 443779 2
none 4833249 10989
unknown 290 0
Total 5536552 11059

Variant Type

Value normal_healthy normal_phenotype
alu deletion 15230 0
alu insertion 269869 1
complex substitution 19726 93
copy number gain 179987 856
copy number loss 294925 1349
copy number variation 153448 0
copy-neutral loss of heterozygosity 26 0
deletion 2627293 6099
delins 687 0
duplication 359303 1197
herv deletion 228 0
herv insertion 229 0
insertion 1393622 165
inversion 108450 390
line1 deletion 3080 0
line1 insertion 46006 0
mobile element deletion 1340 0
mobile element insertion 9379 1
novel sequence insertion 12630 0
sequence alteration 14326 908
sva deletion 1118 0
sva insertion 22028 0
tandem duplication 3622 0
Total 5536552 11059

Data Access

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

Methods

Generating the Presumed Normal Track consists of the following:

References