NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceA Sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... patient Σ0..1Reference(Patient)Who and/or what this is about
... specimen Σ0..1Reference(Specimen)Specimen used for sequencing
... device Σ0..1Reference(Device)The method for sequencing
... quantity Σ0..1QuantityQuantity of the sequence
... species Σ0..1CodeableConceptSupporting tests of human, viruses, and bacteria
SNOMED CT Codes for species (Example)
... referenceSeq Σ0..*BackboneElementReference sequence
.... chromosome Σ0..1CodeableConceptThe chromosome containing the genetic finding
chromosome-human (Example)
.... genomeBuild Σ0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ1..1CodeableConceptReference identifier
ENSEMBL (Example)
.... referenceSeqPointer Σ0..1Reference(Sequence)A Pointer to another Sequence entity as refence sequence
.... referenceSeqString Σ0..1stringA Reference Sequence string
.... windowStart Σ1..1integer0-based start position (inclusive) of the window on the reference sequence
.... windowEnd Σ1..1integer0-based end position (exclusive) of the window on the reference sequence
... variation Σ0..1BackboneElementVariation info in this sequence
.... start Σ0..1integer0-based start position (inclusive) of the variation on the reference sequence
.... end Σ0..1integer0-based end position (exclusive) of the variation on the reference sequence
.... observedAllele Σ0..1stringNucleotide(s)/amino acids from start position to stop position of observed variation
.... referenceAllele Σ0..1stringNucleotide(s)/amino acids from start position to stop position of reference variation
.... cigar Σ0..1stringExtended CIGAR string for aligning the sequence with reference bases
... quality Σ0..*BackboneElementSequence Quality
.... start Σ0..1integer0-based start position (inclusive) of the sequence
.... end Σ0..1integer0-based end position (exclusive) of the sequence
.... score Σ0..1QuantityQuality score
.... method Σ0..1stringMethod for quality
... allelicState Σ0..1CodeableConceptThe level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
LOINC 53034-5 answerlist (Example)
... allelicFrequency Σ0..1decimalAllele frequencies
... copyNumberEvent Σ0..1CodeableConceptCopy Number Event: Values: amplificaiton / deletion / LOH
CopyNumberEvent (Example)
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository Σ0..*BackboneElementExternal repository
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... variantId Σ0..1stringId of the variant
.... readId Σ0..1stringId of the read
... pointer Σ0..*Reference(Sequence)Pointer to next atomic sequence
... observedSeq Σ0..1stringObserved Sequence
... observation Σ0..1Reference(Observation)Observation-genetics
... structureVariation Σ0..1BackboneElement
.... precisionOfBoundaries Σ0..1stringPrecision of boundaries
.... reportedaCGHRatio Σ0..1decimalStructural Variant reported aCGH ratio
.... length Σ0..1integerStructural Variant Length
.... outer Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Outer Start-End
..... end Σ0..1integerStructural Variant Outer Start-End
.... inner Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Inner Start-End
..... end Σ0..1integerStructural Variant Inner Start-End

doco Documentation for this format