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<title>Rs</title>
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<h3>Rs</h3><pre>Defined in file <a href="docsum.asn.html">docsum.asn</a>
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C++ class: <a href="../doxyhtml/classCRs.html">CRs</a>
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Rs ::= SEQUENCE {
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attlist SET {
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rsId INTEGER, --refSNP (rs) number
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snpClass ENUMERATED {
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snp (1),
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in-del (2),
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heterozygous (3),
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microsatellite (4),
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named-locus (5),
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no-variation (6),
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mixed (7),
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multinucleotide-polymorphism (8)
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},
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snpType ENUMERATED {
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notwithdrawn (1),
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artifact (2),
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gene-duplication (3),
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duplicate-submission (4),
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notspecified (5),
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ambiguous-location (6),
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low-map-quality (7)
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},
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molType ENUMERATED {
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genomic (1),
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cDNA (2),
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mito (3),
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chloro (4),
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unknown (5)
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},
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--minimum reported success rate of all submissions in
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-- cluster
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validProbMin INTEGER OPTIONAL,
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--maximum reported success rate of all submissions in
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-- cluster
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validProbMax INTEGER OPTIONAL,
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--at least one genotype reported for this
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-- refSNP
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genotype BOOLEAN OPTIONAL,
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bitField VisibleString OPTIONAL,
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taxId INTEGER OPTIONAL
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},
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het SEQUENCE {
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attlist SET {
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--Est=Estimated average het from allele
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-- frequencies, Obs=Observed from genotype data
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type ENUMERATED {
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est (1),
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obs (2)
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},
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value REAL, --Heterozygosity
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--Standard error of Het
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-- estimate
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stdError REAL OPTIONAL
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},
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het NULL
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} OPTIONAL,
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validation SEQUENCE {
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attlist SET {
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--at least one subsnp in cluster has frequency data
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-- submitted
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byCluster BOOLEAN OPTIONAL,
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byFrequency BOOLEAN OPTIONAL, --Validated by allele frequency
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byOtherPop BOOLEAN OPTIONAL,
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--cluster has 2+ submissions, with 1+ submissions
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-- assayed with a non-computational method
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by2Hit2Allele BOOLEAN OPTIONAL,
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byHapMap BOOLEAN OPTIONAL, --Validated by HapMap <a href="Project.html">Project</a>
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by1000G BOOLEAN OPTIONAL, --Validated by 1000 Genomes <a href="Project.html">Project</a>
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suspect BOOLEAN OPTIONAL --Suspected to be false SNP
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},
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--dbSNP batch-id's for other pop snp validation
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-- data.
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otherPopBatchId SEQUENCE OF INTEGER OPTIONAL,
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--dbSNP batch-id's for double-hit snp
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-- validation data. Use batch-id to get methods, etc.
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twoHit2AlleleBatchId SEQUENCE OF INTEGER OPTIONAL,
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--Frequency validation class (1) low frequency
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-- variation that is cited in journal and other reputable
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-- sources (2) greater than 5 percent minor allele freq in each
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-- and all populations (4) greater than 5 percent minor allele
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-- freq in 1+ populations (8) if the variant has 2+ minor
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-- allele count based on freq or genotype data (16) less than 1
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-- percent minor allele freq in each and all populations (32)
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-- less than 1 percent minor freq in 1+ populations
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frequencyClass SEQUENCE OF INTEGER OPTIONAL,
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--alidated by HapMap <a href="Project.html">Project</a> phase1-genotyped
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-- (1), Phase 1 genotyped; filtered, non-redundant
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-- phase2-genotyped (2), Phase 2 genotyped; filtered,
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-- non-redundant phase3-genotyped (4) Phase 3 genotyped;
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-- filtered, non-redundant
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hapMapPhase SEQUENCE OF INTEGER OPTIONAL,
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--Validated by 1000 Genomes <a href="Project.html">Project</a> (TGP) pilot
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-- 1 (1), pilot 2 (2), pilot 3 (4)
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tGPPhase SEQUENCE OF INTEGER OPTIONAL,
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--Suspected to be false SNP evidence Single
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-- Nucleotide Difference - paralogous genes (1), Genotype or
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-- base calling errors (2), Submission evidence or errors (4),
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-- Others (8)
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suspectEvidence SEQUENCE OF VisibleString OPTIONAL
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},
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--date the refsnp cluster was
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-- instantiated
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--date the refsnp cluster was
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-- instantiated
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create SEQUENCE {
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attlist SET {
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--build number when the cluster was
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-- created
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build INTEGER OPTIONAL,
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date VisibleString OPTIONAL --yyyy-mm-dd
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},
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--date the refsnp cluster was
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-- instantiated
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create NULL
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},
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--most recent date the cluster was updated (member added or
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-- deleted)
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--most recent date the cluster was updated (member added or
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-- deleted)
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update SEQUENCE {
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attlist SET {
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--build number when the cluster was
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-- updated
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build INTEGER OPTIONAL,
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date VisibleString OPTIONAL --yyyy-mm-dd
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},
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--most recent date the cluster was updated (member added or
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-- deleted)
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update NULL
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} OPTIONAL,
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sequence SEQUENCE {
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attlist SET {
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--dbSNP ss# selected as source of refSNP flanking
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-- sequence, ss# part of ss-list below
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exemplarSs INTEGER,
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ancestralAllele VisibleString OPTIONAL
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},
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--5' sequence that flanks the
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-- variation
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seq5 VisibleString OPTIONAL,
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--list of all nucleotide alleles observed in
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-- ss-list members, correcting for reverse complementation of
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-- members reported in reverse orientation
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observed VisibleString,
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--3' sequence that flanks the
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-- variation
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seq3 VisibleString OPTIONAL
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},
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ss SEQUENCE OF <a href="Ss.html">Ss</a>,
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assembly SEQUENCE OF <a href="Assembly.html">Assembly</a> OPTIONAL,
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primarySequence SEQUENCE OF <a href="PrimarySequence.html">PrimarySequence</a> OPTIONAL,
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rsStruct SEQUENCE OF <a href="RsStruct.html">RsStruct</a> OPTIONAL,
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rsLinkout SEQUENCE OF <a href="RsLinkout.html">RsLinkout</a> OPTIONAL,
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mergeHistory SEQUENCE OF SEQUENCE {
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attlist SET {
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--previously issued rs id whose member assays have
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-- now been merged
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rsId INTEGER,
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--build id when rs id was merged into parent
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-- rs
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buildId INTEGER OPTIONAL,
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--TRUE if strand of rs id is reverse to parent
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-- object's current strand
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orientFlip BOOLEAN OPTIONAL
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},
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mergeHistory NULL
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} OPTIONAL,
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hgvs SEQUENCE OF VisibleString OPTIONAL, -- HGVS name list
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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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-- 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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alleleOrigin SEQUENCE OF
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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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-- 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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SEQUENCE {
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attlist SET {
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allele VisibleString OPTIONAL
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},
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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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-- 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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alleleOrigin INTEGER
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} OPTIONAL,
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phenotype SEQUENCE OF SEQUENCE {
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-- unknown (0),
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-- untested (1),
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-- non-pathogenic (2),
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-- probable-non-pathogenic (3),
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-- probable-pathogenic (4),
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-- pathogenic (5),
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-- drug response (6),
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-- other (255)
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clinicalSignificance SEQUENCE OF VisibleString OPTIONAL
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} OPTIONAL,
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bioSource SEQUENCE OF SEQUENCE {
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-- unknown (0) ,
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-- genomic (1) ,
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-- chloroplast (2) ,
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-- chromoplast (3) ,
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-- kinetoplast (4) ,
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-- mitochondrion (5) ,
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-- plastid (6) ,
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-- macronuclear (7) ,
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-- extrachrom (8) ,
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-- plasmid (9) ,
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-- transposon (10) ,
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-- insertion-seq (11) ,
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-- cyanelle (12) ,
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-- proviral (13) ,
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-- virion (14) ,
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-- nucleomorph (15) ,
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-- apicoplast (16) ,
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-- leucoplast (17) ,
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-- proplastid (18) ,
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-- endogenous-virus (19) ,
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-- hydrogenosome (20) ,
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-- chromosome (21) ,
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-- chromatophore (22)
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genome SEQUENCE OF VisibleString OPTIONAL,
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-- unknown (0) ,
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-- natural (1) , normal biological entity
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-- natmut (2) , naturally occurring mutant
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-- mut (3) , artificially mutagenized
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-- artificial (4) , artificially engineered
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-- synthetic (5) , purely synthetic
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-- other (255)
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origin SEQUENCE OF VisibleString OPTIONAL
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} OPTIONAL,
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frequency SEQUENCE OF SEQUENCE {
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attlist SET {
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freq REAL OPTIONAL,
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allele VisibleString OPTIONAL,
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popId INTEGER OPTIONAL, --dbSNP Populaton ID
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sampleSize INTEGER OPTIONAL
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},
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frequency NULL
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} OPTIONAL
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}</pre>
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