NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceInformation about a biological sequence
... identifier Σ0..*IdentifierUnique ID for this particular sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... coordinateSystem Σ1..1integerNumbering used for sequence (0-based or 1-based)
... 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
... referenceSeq Σ0..1BackboneElementReference sequence
.... chromosome Σ0..1CodeableConceptChromosome containing 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
.... strand Σ1..1integerStrand of DNA
.... windowStart Σ1..1integerStart position (inclusive) of the window on the reference sequence
.... windowEnd Σ1..1integerEnd position (exclusive) of the window on the reference sequence
... variant Σ0..*BackboneElementSequence variant
.... start Σ0..1integerStart position (inclusive) of the variant on the reference sequence
.... end Σ0..1integerEnd position (exclusive) of the variant on the reference sequence
.... observedAllele Σ0..1stringAllele that was observed
.... referenceAllele Σ0..1stringAllele of reference sequence
.... cigar Σ0..1stringExtended CIGAR string for aligning the sequence with reference bases
.... variantPointer Σ0..1Reference(Observation)Pointer to observed variant information
... observedSeq Σ0..1stringObserved sequence
... quality Σ0..*BackboneElementSequence quality
.... standardSequence Σ0..1CodeableConceptStandard sequence for comparison
.... start Σ0..1integerStart position (inclusive) of the sequence
.... end Σ0..1integerEnd position (exclusive) of the sequence
.... score Σ0..1QuantityQuality score
.... method Σ0..1CodeableConceptMethod for quality
.... truthTP Σ0..1decimalTrue positives from the perspective of the truth data
.... queryTP Σ0..1decimalTrue positives from the perspective of the query data
.... truthFN Σ0..1decimalFalse negatives
.... queryFP Σ0..1decimalFalse positives
.... gtFP Σ0..1decimalFalse positives where the non-REF alleles in the Truth and Query Call Sets match
.... precision Σ0..1decimalPrecision
.... recall Σ0..1decimalRecall
.... fScore Σ0..1decimalF-score
... 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
... structureVariant Σ0..*BackboneElement
.... 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