dbVar Help

  1. Introduction
  2. Variant Call and Region Types
  3. dbVar Study Browser
  4. dbVar Study page
  5. dbVar Variant page
  6. dbVar Variant rendering
  7. dbVar Placements
  8. FTP site
  9. dbVar Entrez search

Last updated June 2017


Introduction

dbVar is a database of human genomic structural variation where users can search, view, and download data from submitted studies. dbVar stopped supporting data from non-human organisms on November 1, 2017; however existing non-human data remains available via FTP download. In keeping with the common definition of structural variation, most variants are larger than 50 basepairs in length - however a handful of smaller variants may also be found. dbVar provides access to the raw data whenever available, as well as links to additional resources, from both NCBI and elsewhere. For more information on structural variation see the Overview of Structural Variation page. For frequently asked questions see the dbVar FAQ page.

dbVar is a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH) in Bethesda, Maryland.


Variant Call and Region Types

dbVar supports the types of structural variation listed in Table 1 below. Each variant call is submitted using one of the Variant Call Types in the first column; corresponding Sequence Ontology IDs and definitions are listed in the middle column; and Variant Region Types (for regions formed by merging similar calls) are indicated in the last column. (For an explanation of the differences between calls and regions, see our Overview of Structural Variation page.)

Variant Call Type Sequence Ontology ID Variant Region Type

complex substitution

SO:1000005 (complex substitution) When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.

complex substitution

copy number gain

SO:0001742 A sequence alteration whereby the copy number of a given region is greater than the reference sequence.

copy number variation

copy number loss

SO:0001743 A sequence alteration whereby the copy number of a given region is less than the reference sequence.

copy number variation

copy number variation

SO:0001019 A variation that increases or decreases the copy number of a given region.

copy number variation

deletion

SO:0000159 The point at which one or more contiguous nucleotides were excised.

copy number variation

duplication

SO:0001742 (copy number gain) A sequence alteration whereby the copy number of a given region is greater than the reference sequence.

copy number variation

indel

SO:1000005 (complex substitution) When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.

complex

insertion

SO:0000667 The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.

insertion

interchromosomal translocation

SO:0002060 A translocation where the regions involved are from different chromosomes.

translocation, complex chromosomal rearrangement

intrachromosomal translocation

SO:0002061 A translocation where the regions involved are from the same chromosome.

translocation, complex chromosomal rearrangement

inversion

SO:1000036 A continuous nucleotide sequence is inverted in the same position.

inversion

mobile element insertion

SO:0001837 A kind of insertion where the inserted sequence is a mobile element.

mobile element insertion

Alu insertion

SO:0002063 An insertion of sequence from the Alu family of mobile elements.

mobile element insertion

LINE1 insertion

SO:0002064 An insertion from the Line1 family of mobile elements.

mobile element insertion

SVA insertion

SO:0002065 An insertion of sequence from the SVA family of mobile elements.

mobile element insertion

HERV insertion

SO:0002187 An insertion of sequence from the HERV family of mobile elements.

mobile element insertion

novel sequence insertion

SO:0001838 An insertion the sequence of which cannot be mapped to the reference genome.

novel sequence insertion

mobile element deletion

SO:0002066 A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element).

mobile element deletion

Alu deletion

SO:0002070 A deletion of an Alu mobile element with respect to a reference.

mobile element deletion

LINE1 deletion

SO:0002069 A deletion of a LINE1 mobile element with respect to a reference.

mobile element deletion

SVA deletion

SO:0002068 A deletion of an SVA mobile element with respect to a reference.

mobile element deletion

HERV deletion

SO:0002067 A deletion of the HERV mobile element with respect to a reference.

mobile element deletion

sequence alteration

SO:0001059 A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.

sequence alteration

short tandem repeat variation

SO:0002096 A kind of sequence variant whereby a tandem repeat is expanded or contracted with regard to a reference.

short tandem repeat variation

tandem duplication

SO:1000173 A duplication consisting of 2 identical adjacent regions.

tandem duplication
Table 1: Variant Call and Region Types


dbVar Study Browser

Data in dbVar is organized by Study. "Study" typically refers to a publication, however some Studies are community resources which are updated with new data on a regular basis (e.g., Clinical Genome Resource - ClinGen, nstd37). Each Study is given an accession that begins with -std:  nstd if the study was submitted to NCBI and estd if the study was submitted to EBI. The dbVar Study Browser (Figure 1) provides a summary of the studies in dbVar. The browser can be sorted by Study accession, Organism, Study Type, Method, Number of Variant Regions, Number of Variant Calls, or Publication. Links to the Study Page and PubMed summary for each study are provided. Filters to the right of the browser allow you to narrow content by Study Type, Method, or Number of Variant Regions.

study browser

Figure 1: dbVar Study Browser


dbVar Study page

Each Study in dbVar has a Study Page that displays basic information about the study. At the top is a general information section describing basic information about the study, including links to BioProjectsPubMed, dbGaP, and the submitter's lab page (if available). This is followed by a Detailed Information section where you can download variant data for the current study (Variant Regions, Variant Calls, Both, or all via FTP) or browse details about Variant Summary, Samplesets, Experimental Details, or Validations in a tabbed format.

variant summary tab

Figure 2a: General Information and Variant Summary Tab (Study Page)  -   The Variant Summary tab displays the number of Variant Calls and Variant Regions for the current study on each chromosome, Placement type (i.e., whether data is available on the Submitted assembly and/or Remapped assemblies), and links to a graphical display of the variants on NCBI's Sequence Viewer. A pull-down menu above the table allows you to display the current study's data on the submitted assembly, or on any assemblies to which the data has been remapped.

[] Study Page - Samplsets tab

Figure 2b: Samplesets Tab (Study Page)  -  The Samplesets tab describes any logical division of samples in the study. Details include Name, Description, Size, and relevant Phenotypes, if any. Note that additional details about individual subjects in a sampleset can be found by downloading the Samples data. If subjects have not been consented to have their data displayed publicly (as in the example above), clinical information and links between genetic variants are stored behind controlled access at NCBI's dbGaP. Samples and variants are then anonymized before being forwarded to dbVar.

Figure 2c: Experimental Details Tab (Study Page)

Figure 2c: Experimental Details Tab (Study Page)

Figure 2c: Experimental Details Tab (Study Page)  -  The Experimental Details tab provides information on the methods and analyses that were used in the study. Each unique combination of method and analysis is named an "Experiment." A complete list of allowable Method Types and Analysis Types can be found in the Excel submission template, or by clicking here. Experiments can be one of three types: Discovery, Validation, or Genotyping. The Experimental Details tab is also where you can access links to the study's raw data (e.g., sequence traces or array data stored in an external database such as Trace or Array Express).

Figure 2d: Validations Tab (Study Page)

Figure 2d: Validations Tab (Study Page)  -  If validation experiments were performed to confirm variant calls generated by discovery experiments, the validation experiments are assigned unique IDs and are listed along with the relevant method in the Validations tab. Individual validation results can be accessed by downloading the variant data itself from the Study Page. If no validation experiments were performed for a given study, the Validations tab will indicate that no validation data were submitted to dbVar.


dbVar Variant Page

Each dbVar Variant page displays detailed information about an accessioned Variant Region. At the top of the page is a section with general information about the Variant Region (Study, number of supporting Variant Calls, Region size, etc. - see Figure 3a), and a chromosome ideogram displaying the variant's location on the genome. This is followed by a tabbed section with complete variant details:  Genome View, Variant Region Details and Evidence, Validation Information, Clinical Assertions, and Genotype Information (see figure legends below for information on each of these tabs).

Variant Page

Figure 3a: General Information (top) and Genome View Tab (Variant Page)  -  The Genome View Tab shows the current variant in NCBI’s Sequence Viewer in the context of known genes and other variant data from the current study. Use the pull-down menu to select the assembly you want to view. Each black bar represents a Variant Region (the current region is centered and highlighted), while the colored bars represent Variant Calls that support each region.  The display default is to collapse all supporting variant calls, but this can be adjusted (for example, to show all individual calls) by clicking Configure… Variations… Show All. Clicking on any Variant Region or Variant Call will reveal a pop-up tooltip with information about the variant and a link to its dbVar page.

Variant Page – VRDE tab

Figure 3b: Variant Region Details and Evidence Tab (Variant Page)  -  This tab contains placement coordinates for the variant region on the assembly on which the region was originally submitted as well as assemblies to which it was subsequently mapped.  In the case of remapped placements, the Score column indicates the quality of the remap – Perfect, Good, or Pass (for details see dbVar Placements section below). Below the Variant Region information are details on the supporting Variant Calls that were merged to define the Region, including their placements (on Submitted and/or Remapped assemblies). Complete details can always be downloaded using the links above the tabbed section of the Variant Page.

Variant Page – Validation Info tab

Figure 3c: Validation Information Tab (Variant Page)  -  If any Variant Call results were validated with additional methods, this tab provides details on the methods and analyses used in the validation, and the results (Pass or Fail for each call tested).

Variant Page – Clinical Assertions tab

Figure 3d: Clinical Assertions Tab (Variant Page)  -  If in the course of a study an association was established between a Variant Call and a phenotype observed in a Subject, details are provided here.  The Variant Call ID is followed by the sample in which it was observed (with a link if the sample is publicly available), the type of event (insertion, deletion, copy number gain, etc.), the parental origin of the variant if it was determined, the phenotype associated with the variant, and the authors’ assessment of its likely pathogenicity. For a reminder of how studies involving sensitive clinical and genetic information are processed, please refer to the Figure 2b legend above.


dbVar Variant rendering

Rendering Breakpoint Ambiguity

Figure 4a: Rendering breakpoint ambiguity. There are four common scenarios for most variants (either SVs or SSVs) as shown in the table above. However, mixed cases with a defined breakpoint at one end and an undefined breakpoint range at the other end are possible as well. Here, we use (CNV SV) as examples.

Variant Rendering - Examples

Figure 4b: Rendering variant types. Variants are visually represented in several places: the Genome View tab of variant pages; the dbVar Genome Browser; and NCBI's Sequence Viewer. Colors distinguish types of structural variant (copy number gain/loss, insertion, inversion, etc.). Breakpoint ambiguity is represented by translucency and/or arrows at variant ends.


dbVar Placements

Most variants are submitted to dbVar as asserted locations on a particular assembly; this assembly is not always the current assembly. Additionally, all studies have not used the same assembly to do their analysis. In order to be able to compare data from different studies, it is necessary to obtain placements for all variants on the same set of assemblies. For most variants, we do this using the NCBI Remap Service using the following parameters:

  • Minimum ratio of bases that must be remapped: 0.5
  • Maximum ratio for difference between source length and target length: 4.0
  • The 'Merge' function is turned on.
  • Multiple locations can be returned.

We use relatively permissive parameters as many structural variants fall within regions of the genome that are likely to change from assembly to assembly. Additionally, NCBI Remap produces a coverage score that is calculated by taking the length of the feature in the target assembly and dividing it by the length of the feature in the source assembly. A score of 1 suggests the region is relatively unchanged between assemblies (note: single bases aren't assessed); a score of >1 suggests an insertion in the target assembly and a score of <1 suggests a deletion in the target assembly. We provide a qualitative assessment of the remapping status on our web pages:

  • Perfect: coverage score equal to 1
  • Good: coverage score within 5% of 1
  • Pass: coverage deviates from 1 by greater than 5%

A relatively small number of variants submitted to dbVar are defined by sequence. These are typically insertion sequences that could not be placed on the assembly used in the analysis of the study. Such sequences are submitted to GenBank/EMBL/DDBJ and tracked in dbVar using the assigned accession.version. These sequences are aligned to newer assemblies using a process developed in-house called the NG Aligner (unpublished). Sequences that are aligned with >95% coverage and 98% identity are considered placed.

It is in the nature of evolving assemblies that variants called on an earlier assembly sometimes will not map cleanly to a newer (presumably more accurate) assembly. In these situations the Remapper may output multiple alternative placements and, even though they are scored, one cannot know with certainty exactly where, and with what degree of certainty, a variant can be placed on the newer assembly. Therefore dbVar implements a set of rules for filtering remap results, with the goal of providing users our best estimates based on imperfect remapping data. In some cases variants may fail to remap altogether – these are indicated in dbVar FTP download files as having failed remap – and should be considered suspect. More information about assembly-assembly alignments and the meaning of 'First Pass' versus 'Second Pass' can be found on this Remapper page.

Assemblies in scope

dbVar displays placement data for the assembly used in the analysis of a study (the 'Submitted' placement). For most organisms, we will also attempt to find a placement for a variant on the 'current' assembly, if available. When an assembly is updated we will support the 'current' and 'previous' assembly for up to a year. For example, we currently support placements for human data on GRCh37 and GRCh38.


FTP Site

All data in dbVar can be downloaded from our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/. Data is organized by assembly and by study.  A complete listing of available downloads is available online.  If you download by assembly, please be aware that some Variant Calls or Variant Regions may have been submitted on an assembly other than the one being downloaded; these variants will have been remapped to reflect their corresponding placements on the downloaded assembly, placements for which can be found in a separate file in the FTP directory. For example, the GRCh37 assembly download includes all variants that were submitted on GRCh37, plus variants submitted on other assemblies and that were remapped to GRCh37. Remapped status is indicated in the download files.

If you choose to download by assembly, the data are available only in GVF format. If instead you download by study, the data are available in five formats:

GVF:

  • Variant calls
  • Variant regions

VCF:

  • Variant calls
  • Variant regions

TAB:

  • Contacts
  • Experiment
  • Sample
  • Sampleset
  • Study
  • Variant calls
  • Variant regions

CSV:

  • Samples
  • Variant calls
  • Variant regions

XML:

  • Contacts
  • Experiment
  • Sample
  • Sampleset
  • Study
  • Subject
  • Variant calls
  • Variant regions


dbVar Entrez search

A search bar is provided on the top of each dbVar page with a drop-down menu to search dbVar and other NCBI resources using Entrez (See Entrez Help for further details).

A dbVar search returns Studies, with links to the Study page, and Variants, with links to the Variant page. The filters on the right side allow the user to view All results, Study results or Variant results.

The dbVar Advanced search page allows the user to build up an Entrez search query choosing the search fields and values from drop-down menus.

dbVar Search Fields

The following search fields are available to search dbVar:

Accession [ACC, ACCN] Numeric Portion of NCBI Study ID [NST, NSTD, NSTNUM, NSTID]
Accession Version [ACCV, ACCVERS] Numeric Portion of NCBI Variant Call ID [NSSV, NSSVNUM, NSSVID]
Alignments used for remapped placement [RALN, Alignment] Numeric Portion of NCBI Variant Region ID [NSV, NSVNUM, NSVID]
Allele Origin [ALOR, ORIGIN, ALLORGN] Object Type [OT]
All fields [ALL] Organism [ORG, ORGN]
Assembly Accession [ASAC, ASSMACC, ASSMACCN, ASM_ACC] Phenotype [PHEN, PHNO, PHENO, PTYPE]
Assembly Filter [ASMF] Placement rank within the major assembly [RANK]
Assembly Name [ASSM, ASSMBLY] Placement Type [PTYP, PL_TYPE]
Assembly Organism [AORG, ASM_ORGN, ASM_ORG] PMID [PMID, PUBMED_ID]
Assembly Taxonomy ID [ATAX, ASM_TAXID, ASM_TAX_ID] Publication Date [PDAT, PUBDAT]
Author [AUTH] Remap Coverage [COVG, Coverage]
BioProject ID [GPRJ, BIOID, BIOPROJECT] Remap Failure Code [FAIL]
BioProject Name [PRNM, BIONAM, PROJECT] Sample [SMPL]
Chromosome [CH, CHRNUM, CHROM, CHROMOSOME] Sample Count [SC, SCOUNT, SAMCOUNT]
Chromosome Accession [CHRA, CHRACC, CHR_ACC, CHROM_ACCESSION] Study Accession [ST, STACC, STUDY_ACCESSION]
Chromosome End [CHRE, END, CHREND, CHR_STOP] Study Description [STDE, STUDY_DESC]
Chromosome Inner End [INRE, INNER_END, CHR_INNER_STOP] Study Display Name [STDN, STUDY_DISP]
Chromosome Inner Start [INRS, INNER_START] Study ID [STDY, STUDY, STUDYID]
Chromosome Outer End [OTRE, OUTER_END, CHR_OUTER_STOP] Study Type [STYP, STYPE, STUDYTYPE]
Chromosome Outer Start [OTRS, OUTER_START] Subject Phenotype status [SUPH, SUPSTA, SUB_PSTAT, SUB_PHENSTAT]
Chromosome Start [CHRS, START, CHRSTART] Submitter Affiliation [LAB, CENTER]
Detection Method [DET, DETECTION] Submitter MyNCBI ID [NCBI, myNCBI]
Filter [FILTER] Submitter Name [SUB, SUBM]
Gender [SEX,GNDR] Submitter Variant ID [SVAR, SUBVAR, SVARID, SUBVARID]
Gene Full Name [GDSC, GENED, GENEFN, GENE_DESC, GENE_FULL] Taxonomy ID [TXID, TAXID, TAXONOMY_ID, TAXONOMY]
Gene Name [GENE, GENE_NAME, SYM] UID [UID]
Library Abbreviation [LIB, LIBRARY, LIBNAME] Unplaced Contig Accession [CTG, CONTIG, CTG_ACC, CTG_ACCESSION]
MeSH Terms [MESH, MH] Validation Method [VAL, VALIDATION]
MeSH Unique ID [MESH_ID, MHUI, MeSHUI] Validation Result [VSTA, VSTAT, VALSTAT, VALIDATIONSTAT, VALIDATIONSTATUS]
Method Platform [MPLT, METHPLAT, PLATFORM] Validation Result Weight [VWGT, VALSTAT_WEIGHT]
Method Submission Name [MSUB] Variant Call Accession [SSV, SSVACC, SSV_ACCESSION]
Method Type [METH, METHOD] Variant Call Count [SSVC, SSVCOUNT, SUPVARCOUNT, VC_COUNT]
Method Type Category [MCAT, METHOD_CATEGORY] Variant Call Type [CLTP, VCTYPE, SSVTYPE, CALLTYPE]
Method Type Weight [MWGT, METHOD_WEIGHT] Variant Clinical Assertion [CLIN, CLIN_SIG, CLINICAL_ASSERTION, ASSERT]
MIM_id [MIM, OMIM] Variant Description [DESC]
Modification Date [MDAT, UDAT, UPDATE, UDATE, MODATE, UPDATEDATE] Variant Region Accession [SV, SVACC, SV_ACCESSION]
Multiple in assembly [MULT] Variant Region Count [VC, VCOUNT, VARCOUNT]
Numeric Portion of EBI Study ID [ESTD, ESTNUM, ESTID] Variant Region Type [VT, VTYPE, VARTYPE, VRTYPE, SVTYPE]
Numeric Portion of EBI Variant Call ID [ESSV, ESSVNUM, ESSVID] Variant Size [VLEN, VSIZE, VARSIZE, VARLEN, VARLENGTH]
Numeric Portion of EBI Variant Region ID [ESV, ESVNUM, ESVID] Variant Zygosity [Zygosity, ZYG]

Accession [ACC, ACCN]

Accession of any internal or external identifier. Versions removed from GENBANK accessions.

Accession Version [ACCV, ACCVERS]

Accession and version of GENBANK accessions used in variant sequence or support.

Alignments used for remapped placement [RALN, Alignment]

Indicates whether the remapped placement is based on First Pass or Second Pass alignments.

Allele Origin [ALOR, ORIGIN, ALLORGN]

Allele origin (controlled vocabulary), including Both=Germline+Somatic

All fields [ALL]

Default.

Assembly Accession [ASAC, ASSMACC, ASSMACCN, ASM_ACC]

Assembly accession of placement

Assembly Filter [ASMF]

Major Assembly of placement with (UCSC name)

Assembly Name [ASSM, ASSMBLY]

Assembly of placement

Assembly Organism [AORG, ASM_ORGN, ASM_ORG]

Assembly organism names (exploded)

Assembly Taxonomy ID [ATAX, ASM_TAXID, ASM_TAX_ID]

Assembly taxonomy ID

Author [AUTH]

All authors included in journal

BioProject ID [GPRJ, BIOID, BIOPROJECT]

Unique identifier from BioProjects

BioProject Name [PRNM, BIONAM, PROJECT]

Name from BioProjects corresponding to BioProject_ID

Chromosome [CH, CHRNUM, CHROM, CHROMOSOME]

Chromosome of placement

Chromosome Accession [CHRA, CHRACC, CHR_ACC, CHROM_ACCESSION]

Chromosome of placement, using accession.version

Chromosome End [CHRE, END, CHREND, CHR_STOP]

End of placement on chromosome

Chromosome Inner End [INRE, INNER_END, CHR_INNER_STOP]

Inner end of placement on chromosome

Chromosome Inner Start [INRS, INNER_START]

Inner start of placement on chromosome

Chromosome Outer End [OTRE, OUTER_END, CHR_OUTER_STOP]

Outer end of placement on chromosome

Chromosome Outer Start [OTRS, OUTER_START]

Outer start of placement on chromosome

Chromosome Start [CHRS, START, CHRSTART]

Start of placement on chromosome

Detection Method [DET, DETECTION]

Detection method

Filter [FILTER]

Filter to return All records, just Study records or just Variant records.

Gender [SEX,GNDR]

Subject gender (controlled vocabulary)

Gene Full Name [GDSC, GENED, GENEFN, GENE_DESC, GENE_FULL]

Full name (description) of gene at same location as variant

Gene Name [GENE, GENE_NAME, SYM]

Name or alias of gene at same location as variant

Library Abbreviation [LIB, LIBRARY, LIBNAME]

Library name used in the Method

MeSH Terms [MESH, MH]

Medical Subject Headings assigned to publication

MeSH Unique ID [MESH_ID, MHUI, MeSHUI]

NLM MeSH Browser Unique ID

Method Platform [MPLT, METHPLAT, PLATFORM]

Method platform

Method Submission Name [MSUB]

Submission name of individual method, used when study contains multiple methods from different submitters, as does the curated dataset.

Method Type [METH, METHOD]

Method type (controlled vocabulary)

Method Type Category [MCAT, METHOD_CATEGORY]

Used for sorting and display. Methods are categorized as: probe, mapping, sequencing.

Method Type Weight [MWGT, METHOD_WEIGHT]

Used for sorting. BAC all Method_type values of study or variant are BAC aCGH, Non-BAC study or variant has at least 1 method_type that is other than BAC aCGH

MIM_id [MIM, OMIM]

MIM number.

Modification Date [MDAT, UDAT, UPDATE, UDATE, MODATE, UPDATEDATE]

dbVar Modification Date

Multiple in assembly [MULT]

Boolean indication that placement is a single or one of multiple placements within the major assembly: 0 single; 1 multiple

Numeric Portion of EBI Study ID [ESTD, ESTNUM, ESTID]

Numeric portion of EBI Study ID (estd)

Numeric Portion of EBI Variant Call ID [ESSV, ESSVNUM, ESSVID]

Numeric portion of EBI Variant Call ID (essv)

Numeric Portion of EBI Variant Region ID [ESV, ESVNUM, ESVID]

Numeric portion of EBI Variant Region ID (esv)

Numeric Portion of NCBI Study ID [NST, NSTD, NSTNUM, NSTID]

Numeric portion of NCBI Study ID (nstd)

Numeric Portion of NCBI Variant Call ID [NSSV, NSSVNUM, NSSVID]

Numeric portion of NCBI Variant Call ID (nssv)

Numeric Portion of NCBI Variant Region ID [NSV, NSVNUM, NSVID]

Numeric portion of NCBI Variant Region ID (nsv)

Object Type [OT]

Object type in dbVar (STUDY, VARIANT)

Organism [ORG, ORGN]

Organism name (exploded)

Phenotype [PHEN, PHNO, PHENO, PTYPE]

Phenotype of sample/subject study or reference specimen

Placement rank within the major assembly [RANK]

Placement rank (controlled vocabulary)

Placement Type [PTYP, PL_TYPE]

Placement type (controlled vocabulary)

PMID [PMID, PUBMED_ID]

Unique identifier from PubMed

Publication Date [PDAT, PUBDAT]

Journal Publication date

Remap Coverage [COVG, Coverage]

Remap coverage value (1.0 is perfect).

Remap Failure Code [FAIL]

Reason for remapper failure (controlled vocabulary)

Sample [SMPL]

Sample/subject ID of study or reference specimen

Sample Count [SC, SCOUNT, SAMCOUNT]

Number of samples in study

Study Accession [ST, STACC, STUDY_ACCESSION]

Study dbVar ID (estd or nstd)

Study Description [STDE, STUDY_DESC]

Study description

Study Display Name [STDN, STUDY_DISP]

Study display name

Study ID [STDY, STUDY, STUDYID]

Study, batch or submission ID

Study Type [STYP, STYPE, STUDYTYPE]

Study type assigned by NCBI

Subject Phenotype status [SUPH, SUPSTA, SUB_PSTAT, SUB_PHENSTAT]

Boolean subject phenotype status: 0 not affected/null; 1 affected

Submitter Affiliation [LAB, CENTER]

Submitter's affiliation name

Submitter MyNCBI ID [NCBI, myNCBI]

Submitter login ID in myNCBI system

Submitter Name [SUB, SUBM]

Submitter first and last name

Submitter Variant ID [SVAR, SUBVAR, SVARID, SUBVARID]

Originally submitted variant identifier

Taxonomy ID [TXID, TAXID, TAXONOMY_ID, TAXONOMY]

Taxonomy ID

UID [UID]

UID

Unplaced Contig Accession [CTG, CONTIG, CTG_ACC, CTG_ACCESSION]

Contig of placement, when not on a chromosome, using accession.version

Validation Method [VAL, VALIDATION]

Validation method (controlled vocabulary)

Validation Result [VSTA, VSTAT, VALSTAT, VALIDATIONSTAT, VALIDATIONSTATUS]

Boolean validation status: null not validated, 0 validated with result 0; 1 validated with result 1

Validation Result Weight [VWGT, VALSTAT_WEIGHT]

0 not validated, 1 validated with result 0; 2 validated with result 1

Variant Call Accession [SSV, SSVACC, SSV_ACCESSION]

dbVar ID (essv or nssv) of Variant Call

Variant Call Count [SSVC, SSVCOUNT, SUPVARCOUNT, VC_COUNT]

Number of supporting variant calls in variant region

Variant Call Type [CLTP, VCTYPE, SSVTYPE, CALLTYPE]

Variant Call type (controlled vocabulary)

Variant Clinical Assertion [CLIN, CLIN_SIG, CLINICAL_ASSERTION, ASSERT]

Clinical assertion of a variant (controlled vocabulary)

Variant Description [DESC]

Variant description

Variant Region Accession [SV, SVACC, SV_ACCESSION]

dbVar ID (esv or nsv) of Variant Region

Variant Region Count [VC, VCOUNT, VARCOUNT]

Number of variant regions in study

Variant Region Type [VT, VTYPE, VARTYPE, VRTYPE, SVTYPE]

Variant region type (controlled vocabulary)

Variant Size [VLEN, VSIZE, VARSIZE, VARLEN, VARLENGTH]

Size of variant

Variant Zygosity [Zygosity, ZYG]

Zygosity of a variant (controlled vocabulary)

Support Center

Last updated: 2017-12-20T19:33:04Z