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<title>Variation-ref</title>
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<h3>Variation-ref</h3><pre>Defined in file <a href="seqfeat.asn.html">seqfeat.asn</a>
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C++ class: <a href="../doxyhtml/classCVariation__ref.html">CVariation_ref</a>
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Variation-ref ::= SEQUENCE {
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-- ids (i.e., SNP rsid / ssid, dbVar nsv/nssv)
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-- expected values include 'dbSNP|rs12334', 'dbSNP|ss12345', 'dbVar|nsv1'
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--
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-- we relate three kinds of IDs here:
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-- - our current object's id
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-- - the id of this object's parent, if it exists
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-- - the sample ID that this item originates from
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id <a href="Dbtag.html">Dbtag</a> OPTIONAL,
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parent-id <a href="Dbtag.html">Dbtag</a> OPTIONAL,
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sample-id <a href="Object-id.html">Object-id</a> OPTIONAL,
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other-ids SET OF <a href="Dbtag.html">Dbtag</a> OPTIONAL,
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-- names and synonyms
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-- some variants have well-known canonical names and possible accepted
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-- synonyms
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name VisibleString OPTIONAL,
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synonyms SET OF VisibleString OPTIONAL,
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-- tag for comment and descriptions
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description VisibleString OPTIONAL,
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-- phenotype
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phenotype SET OF <a href="Phenotype.html">Phenotype</a> OPTIONAL,
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-- sequencing / acuisition method
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method SET OF INTEGER {
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unknown (0),
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bac-acgh (1),
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computational (2),
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curated (3),
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digital-array (4),
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expression-array (5),
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fish (6),
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flanking-sequence (7),
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maph (8),
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mcd-analysis (9),
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mlpa (10),
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oea-assembly (11),
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oligo-acgh (12),
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paired-end (13),
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pcr (14),
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qpcr (15),
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read-depth (16),
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roma (17),
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rt-pcr (18),
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sage (19),
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sequence-alignment (20),
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sequencing (21),
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snp-array (22),
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snp-genoytyping (23),
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southern (24),
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western (25),
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optical-mapping (26),
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other (255)
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} OPTIONAL,
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-- Note about SNP representation and pretinent fields: allele-frequency,
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-- population, quality-codes:
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-- The case of multiple alleles for a SNP would be described by
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-- parent-feature of type Variation-set.diff-alleles, where the child
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-- features of type <a href="Variation-inst.html">Variation-inst</a>, all at the same location, would
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-- describe individual alleles.
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-- population data
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-- DEPRECATED - do not use
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population-data SET OF <a href="Population-data.html">Population-data</a> OPTIONAL,
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-- variant properties bit fields
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variant-prop <a href="VariantProperties.html">VariantProperties</a> OPTIONAL,
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-- has this variant been validated?
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-- DEPRECATED: new field = <a href="VariantProperties.html">VariantProperties</a>.other-validation
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validated BOOLEAN OPTIONAL,
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-- link-outs to GeneTests database
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-- DEPRECATED - do not use
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clinical-test SET OF <a href="Dbtag.html">Dbtag</a> OPTIONAL,
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-- origin of this allele, if known
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-- note that these are powers-of-two, and represent bits; thus, we can
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-- represent more than one state simultaneously through a bitwise OR
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-- DEPRECATED: new field = <a href="VariantProperties.html">VariantProperties</a>.allele-origin
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allele-origin INTEGER {
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unknown (0),
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germline (1),
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somatic (2),
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inherited (4),
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paternal (8),
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maternal (16),
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de-novo (32),
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biparental (64),
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uniparental (128),
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not-tested (256),
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tested-inconclusive (512),
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-- stopper - 2^31
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other (1073741824)
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} OPTIONAL,
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-- observed allele state, if known
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-- DEPRECATED: new field = <a href="VariantProperties.html">VariantProperties</a>.allele-state
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allele-state INTEGER {
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unknown (0),
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homozygous (1),
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heterozygous (2),
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hemizygous (3),
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nullizygous (4),
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other (255)
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} OPTIONAL,
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-- NOTE:
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-- 'allele-frequency' here refers to the minor allele frequency of the
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-- default population
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-- DEPRECATED: new field = <a href="VariantProperties.html">VariantProperties</a>.allele-frequency
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allele-frequency REAL OPTIONAL,
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-- is this variant the ancestral allele?
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-- DEPRECATED: new field = <a href="VariantProperties.html">VariantProperties</a>.is-ancestral-allele
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is-ancestral-allele BOOLEAN OPTIONAL,
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-- publication support.
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-- Note: made this pub instead of pub-equiv, since
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-- <a href="Pub.html">Pub</a> can be pub-equiv and pub-equiv is a set of pubs, but it looks like
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-- <a href="Pub.html">Pub</a> is more often used as top-level container
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-- DEPRECATED - do not use; use <a href="Seq-feat.html">Seq-feat</a>.dbxref instead
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pub <a href="Pub.html">Pub</a> OPTIONAL,
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data CHOICE {
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unknown NULL,
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note VisibleString, --free-form
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uniparental-disomy NULL,
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-- actual sequence-edit at feat.location
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instance <a href="Variation-inst.html">Variation-inst</a>,
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-- Set of related Variations.
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-- Location of the set equals to the union of member locations
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set SEQUENCE {
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type INTEGER {
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unknown (0),
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compound (1), -- complex change at the same location on the
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-- same molecule
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products (2), -- different products arising from the same
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-- variation in a precursor, e.g. r.[13g>a,
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-- 13_88del]
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haplotype (3), -- changes on the same allele, e.g
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-- r.[13g>a;15u>c]
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genotype (4), -- changes on different alleles in the same
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-- genotype, e.g. g.[476C>T]+[476C>T]
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mosaic (5), -- different genotypes in the same individual
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individual (6), -- same organism; allele relationship unknown,
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-- e.g. g.[476C>T(+)183G>C]
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population (7), -- population
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alleles (8), -- set represents a set of observed alleles
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package (9), -- set represents a package of observations at
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-- a given location, generally containing
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-- asserted + reference
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other (255)
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},
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variations SET OF <a href="Variation-ref.html">Variation-ref</a>,
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name VisibleString OPTIONAL
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},
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-- variant is a complex and undescribed change at the location
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-- This type of variant is known to occur in dbVar submissions
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complex NULL
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},
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consequence SET OF CHOICE {
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unknown NULL,
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splicing NULL, --some effect on splicing
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note VisibleString, --freeform
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-- Describe resulting variation in the product, e.g. missense,
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-- nonsense, silent, neutral, etc in a protein, that arises from
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-- THIS variation.
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variation <a href="Variation-ref.html">Variation-ref</a>,
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-- see http://www.hgvs.org/mutnomen/recs-prot.html
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frameshift SEQUENCE {
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phase INTEGER OPTIONAL,
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x-length INTEGER OPTIONAL
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},
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loss-of-heterozygosity SEQUENCE {
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-- In germline comparison, it will be reference genome assembly
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-- (default) or reference/normal population. In somatic mutation,
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-- it will be a name of the normal tissue.
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reference VisibleString OPTIONAL,
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-- Name of the testing subject type or the testing tissue.
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test VisibleString OPTIONAL
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}
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} OPTIONAL,
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-- Observed location, if different from the parent set or feature.location.
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-- DEPRECATED - do not use
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location <a href="Seq-loc.html">Seq-loc</a> OPTIONAL,
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-- reference other locs, e.g. mapped source
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-- DEPRECATED - do not use
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ext-locs SET OF <a href="Ext-loc.html">Ext-loc</a> OPTIONAL,
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-- DEPRECATED - do not use; use <a href="Seq-feat.html">Seq-feat</a>.exts instead
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ext <a href="User-object.html">User-object</a> OPTIONAL,
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somatic-origin SET OF SEQUENCE {
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-- description of the somatic origin itself
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source <a href="SubSource.html">SubSource</a> OPTIONAL,
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-- condition related to this origin's type
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condition SEQUENCE {
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description VisibleString OPTIONAL,
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-- reference to BioTerm / other descriptive database
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object-id SET OF <a href="Dbtag.html">Dbtag</a> OPTIONAL
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} OPTIONAL
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} OPTIONAL
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}</pre>
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