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<h3>Rs</h3><pre>Defined in file <a href="docsum.asn.html">docsum.asn</a>
C++ class: <a href="../doxyhtml/classCRs.html">CRs</a>
Rs ::= SEQUENCE {
attlist SET {
rsId INTEGER, --refSNP (rs) number
snpClass ENUMERATED {
snp (1),
in-del (2),
heterozygous (3),
microsatellite (4),
named-locus (5),
no-variation (6),
mixed (7),
multinucleotide-polymorphism (8)
},
snpType ENUMERATED {
notwithdrawn (1),
artifact (2),
gene-duplication (3),
duplicate-submission (4),
notspecified (5),
ambiguous-location (6),
low-map-quality (7)
},
molType ENUMERATED {
genomic (1),
cDNA (2),
mito (3),
chloro (4),
unknown (5)
},
--minimum reported success rate of all submissions in
-- cluster
validProbMin INTEGER OPTIONAL,
--maximum reported success rate of all submissions in
-- cluster
validProbMax INTEGER OPTIONAL,
--at least one genotype reported for this
-- refSNP
genotype BOOLEAN OPTIONAL,
bitField VisibleString OPTIONAL,
taxId INTEGER OPTIONAL
},
het SEQUENCE {
attlist SET {
--Est=Estimated average het from allele
-- frequencies, Obs=Observed from genotype data
type ENUMERATED {
est (1),
obs (2)
},
value REAL, --Heterozygosity
--Standard error of Het
-- estimate
stdError REAL OPTIONAL
},
het NULL
} OPTIONAL,
validation SEQUENCE {
attlist SET {
--at least one subsnp in cluster has frequency data
-- submitted
byCluster BOOLEAN OPTIONAL,
byFrequency BOOLEAN OPTIONAL, --Validated by allele frequency
byOtherPop BOOLEAN OPTIONAL,
--cluster has 2+ submissions, with 1+ submissions
-- assayed with a non-computational method
by2Hit2Allele BOOLEAN OPTIONAL,
byHapMap BOOLEAN OPTIONAL, --Validated by HapMap <a href="Project.html">Project</a>
by1000G BOOLEAN OPTIONAL, --Validated by 1000 Genomes <a href="Project.html">Project</a>
suspect BOOLEAN OPTIONAL --Suspected to be false SNP
},
--dbSNP batch-id's for other pop snp validation
-- data.
otherPopBatchId SEQUENCE OF INTEGER OPTIONAL,
--dbSNP batch-id's for double-hit snp
-- validation data. Use batch-id to get methods, etc.
twoHit2AlleleBatchId SEQUENCE OF INTEGER OPTIONAL,
--Frequency validation class (1) low frequency
-- variation that is cited in journal and other reputable
-- sources (2) greater than 5 percent minor allele freq in each
-- and all populations (4) greater than 5 percent minor allele
-- freq in 1+ populations (8) if the variant has 2+ minor
-- allele count based on freq or genotype data (16) less than 1
-- percent minor allele freq in each and all populations (32)
-- less than 1 percent minor freq in 1+ populations
frequencyClass SEQUENCE OF INTEGER OPTIONAL,
--alidated by HapMap <a href="Project.html">Project</a> phase1-genotyped
-- (1), Phase 1 genotyped; filtered, non-redundant
-- phase2-genotyped (2), Phase 2 genotyped; filtered,
-- non-redundant phase3-genotyped (4) Phase 3 genotyped;
-- filtered, non-redundant
hapMapPhase SEQUENCE OF INTEGER OPTIONAL,
--Validated by 1000 Genomes <a href="Project.html">Project</a> (TGP) pilot
-- 1 (1), pilot 2 (2), pilot 3 (4)
tGPPhase SEQUENCE OF INTEGER OPTIONAL,
--Suspected to be false SNP evidence Single
-- Nucleotide Difference - paralogous genes (1), Genotype or
-- base calling errors (2), Submission evidence or errors (4),
-- Others (8)
suspectEvidence SEQUENCE OF VisibleString OPTIONAL
},
--date the refsnp cluster was
-- instantiated
--date the refsnp cluster was
-- instantiated
create SEQUENCE {
attlist SET {
--build number when the cluster was
-- created
build INTEGER OPTIONAL,
date VisibleString OPTIONAL --yyyy-mm-dd
},
--date the refsnp cluster was
-- instantiated
create NULL
},
--most recent date the cluster was updated (member added or
-- deleted)
--most recent date the cluster was updated (member added or
-- deleted)
update SEQUENCE {
attlist SET {
--build number when the cluster was
-- updated
build INTEGER OPTIONAL,
date VisibleString OPTIONAL --yyyy-mm-dd
},
--most recent date the cluster was updated (member added or
-- deleted)
update NULL
} OPTIONAL,
sequence SEQUENCE {
attlist SET {
--dbSNP ss# selected as source of refSNP flanking
-- sequence, ss# part of ss-list below
exemplarSs INTEGER,
ancestralAllele VisibleString OPTIONAL
},
--5' sequence that flanks the
-- variation
seq5 VisibleString OPTIONAL,
--list of all nucleotide alleles observed in
-- ss-list members, correcting for reverse complementation of
-- members reported in reverse orientation
observed VisibleString,
--3' sequence that flanks the
-- variation
seq3 VisibleString OPTIONAL
},
ss SEQUENCE OF <a href="Ss.html">Ss</a>,
assembly SEQUENCE OF <a href="Assembly.html">Assembly</a> OPTIONAL,
primarySequence SEQUENCE OF <a href="PrimarySequence.html">PrimarySequence</a> OPTIONAL,
rsStruct SEQUENCE OF <a href="RsStruct.html">RsStruct</a> OPTIONAL,
rsLinkout SEQUENCE OF <a href="RsLinkout.html">RsLinkout</a> OPTIONAL,
mergeHistory SEQUENCE OF SEQUENCE {
attlist SET {
--previously issued rs id whose member assays have
-- now been merged
rsId INTEGER,
--build id when rs id was merged into parent
-- rs
buildId INTEGER OPTIONAL,
--TRUE if strand of rs id is reverse to parent
-- object's current strand
orientFlip BOOLEAN OPTIONAL
},
mergeHistory NULL
} OPTIONAL,
hgvs SEQUENCE OF VisibleString OPTIONAL, -- HGVS name list
-- origin of this allele, if known
-- note that these are powers-of-two, and represent bits; thus, we can
-- represent more than one state simultaneously through a bitwise OR
-- unknown (0),
-- germline (1),
-- somatic (2),
-- inherited (4),
-- paternal (8),
-- maternal (16),
-- de-novo (32),
-- biparental (64),
-- uniparental (128),
-- not-tested (256),
-- tested-inconclusive (512),
alleleOrigin SEQUENCE OF
-- origin of this allele, if known
-- note that these are powers-of-two, and represent bits; thus, we can
-- represent more than one state simultaneously through a bitwise OR
-- unknown (0),
-- germline (1),
-- somatic (2),
-- inherited (4),
-- paternal (8),
-- maternal (16),
-- de-novo (32),
-- biparental (64),
-- uniparental (128),
-- not-tested (256),
-- tested-inconclusive (512),
SEQUENCE {
attlist SET {
allele VisibleString OPTIONAL
},
-- origin of this allele, if known
-- note that these are powers-of-two, and represent bits; thus, we can
-- represent more than one state simultaneously through a bitwise OR
-- unknown (0),
-- germline (1),
-- somatic (2),
-- inherited (4),
-- paternal (8),
-- maternal (16),
-- de-novo (32),
-- biparental (64),
-- uniparental (128),
-- not-tested (256),
-- tested-inconclusive (512),
alleleOrigin INTEGER
} OPTIONAL,
phenotype SEQUENCE OF SEQUENCE {
-- unknown (0),
-- untested (1),
-- non-pathogenic (2),
-- probable-non-pathogenic (3),
-- probable-pathogenic (4),
-- pathogenic (5),
-- drug response (6),
-- other (255)
clinicalSignificance SEQUENCE OF VisibleString OPTIONAL
} OPTIONAL,
bioSource SEQUENCE OF SEQUENCE {
-- unknown (0) ,
-- genomic (1) ,
-- chloroplast (2) ,
-- chromoplast (3) ,
-- kinetoplast (4) ,
-- mitochondrion (5) ,
-- plastid (6) ,
-- macronuclear (7) ,
-- extrachrom (8) ,
-- plasmid (9) ,
-- transposon (10) ,
-- insertion-seq (11) ,
-- cyanelle (12) ,
-- proviral (13) ,
-- virion (14) ,
-- nucleomorph (15) ,
-- apicoplast (16) ,
-- leucoplast (17) ,
-- proplastid (18) ,
-- endogenous-virus (19) ,
-- hydrogenosome (20) ,
-- chromosome (21) ,
-- chromatophore (22)
genome SEQUENCE OF VisibleString OPTIONAL,
-- unknown (0) ,
-- natural (1) , normal biological entity
-- natmut (2) , naturally occurring mutant
-- mut (3) , artificially mutagenized
-- artificial (4) , artificially engineered
-- synthetic (5) , purely synthetic
-- other (255)
origin SEQUENCE OF VisibleString OPTIONAL
} OPTIONAL,
frequency SEQUENCE OF SEQUENCE {
attlist SET {
freq REAL OPTIONAL,
allele VisibleString OPTIONAL,
popId INTEGER OPTIONAL, --dbSNP Populaton ID
sampleSize INTEGER OPTIONAL
},
frequency NULL
} OPTIONAL
}</pre>
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