Rs

Defined in file docsum.asn
C++ class: CRs


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 Project 
      by1000G BOOLEAN OPTIONAL, --Validated by 1000 Genomes Project
      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 Project 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 Project (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 Ss,
  assembly SEQUENCE OF Assembly OPTIONAL,
  primarySequence SEQUENCE OF PrimarySequence OPTIONAL,
  rsStruct SEQUENCE OF RsStruct OPTIONAL,
  rsLinkout SEQUENCE OF RsLinkout 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
}