http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1

Raw data describing a biological sequence.

Structure JSON Dependencies FHIRSchema Other Versions Dependant (0)Elements Summary

Name	Flags	Card	Type	Description & Constraints
MolecularSequence		0..*		Information about a biological sequence
identifier	Σ	0..*	Identifier	Unique ID for this particular sequence. This is a FHIR-defined id
type	Σ	0..1	code	aa \| dna \| rna sequenceType (required)
coordinateSystem *	Σ	1..1	integer	Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
patient	Σ	0..1	Reference	Who and/or what this is about
specimen	Σ	0..1	Reference	Specimen used for sequencing
device	Σ	0..1	Reference	The method for sequencing
performer	Σ	0..1	Reference	Who should be responsible for test result
quantity	Σ	0..1	Quantity	The number of copies of the sequence of interest. (RNASeq)
referenceSeq	Σ	0..1	BackboneElement	A sequence used as reference
chromosome	Σ	0..1	CodeableConcept	Chromosome containing genetic finding chromosome-human (example)
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
orientation	Σ	0..1	code	sense \| antisense orientationType (required)
referenceSeqId	Σ	0..1	CodeableConcept	Reference identifier sequenceReference (example)
referenceSeqPointer	Σ	0..1	Reference	A pointer to another MolecularSequence entity as reference sequence
referenceSeqString	Σ	0..1	string	A string to represent reference sequence
strand	Σ	0..1	code	watson \| crick strandType (required)
windowStart	Σ	0..1	integer	Start position of the window on the reference sequence
windowEnd	Σ	0..1	integer	End position of the window on the reference sequence
variant	Σ	0..*	BackboneElement	Variant in sequence
start	Σ	0..1	integer	Start position of the variant on the reference sequence
end	Σ	0..1	integer	End position of the variant on the reference sequence
observedAllele	Σ	0..1	string	Allele that was observed
referenceAllele	Σ	0..1	string	Allele in the reference sequence
cigar	Σ	0..1	string	Extended CIGAR string for aligning the sequence with reference bases
variantPointer	Σ	0..1	Reference	Pointer to observed variant information
observedSeq	Σ	0..1	string	Sequence that was observed
quality	Σ	0..*	BackboneElement	An set of value as quality of sequence
type *	Σ	1..1	code	indel \| snp \| unknown qualityType (required)
standardSequence	Σ	0..1	CodeableConcept	Standard sequence for comparison qualityStandardSequence (example)
start	Σ	0..1	integer	Start position of the sequence
end	Σ	0..1	integer	End position of the sequence
score	Σ	0..1	Quantity	Quality score for the comparison
method	Σ	0..1	CodeableConcept	Method to get quality qualityMethod (example)
truthTP	Σ	0..1	decimal	True positives from the perspective of the truth data
queryTP	Σ	0..1	decimal	True positives from the perspective of the query data
truthFN	Σ	0..1	decimal	False negatives
queryFP	Σ	0..1	decimal	False positives
gtFP	Σ	0..1	decimal	False positives where the non-REF alleles in the Truth and Query Call Sets match
precision	Σ	0..1	decimal	Precision of comparison
recall	Σ	0..1	decimal	Recall of comparison
fScore	Σ	0..1	decimal	F-score
roc	Σ	0..1	BackboneElement	Receiver Operator Characteristic (ROC) Curve
score	Σ	0..*	integer	Genotype quality score
numTP	Σ	0..*	integer	Roc score true positive numbers
numFP	Σ	0..*	integer	Roc score false positive numbers
numFN	Σ	0..*	integer	Roc score false negative numbers
precision	Σ	0..*	decimal	Precision of the GQ score
sensitivity	Σ	0..*	decimal	Sensitivity of the GQ score
fMeasure	Σ	0..*	decimal	FScore of the GQ score
readCoverage	Σ	0..1	integer	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	Σ	0..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
type *	Σ	1..1	code	directlink \| openapi \| login \| oauth \| other repositoryType (required)
url	Σ	0..1	uri	URI of the repository
name	Σ	0..1	string	Repository's name
datasetId	Σ	0..1	string	Id of the dataset that used to call for dataset in repository
variantsetId	Σ	0..1	string	Id of the variantset that used to call for variantset in repository
readsetId	Σ	0..1	string	Id of the read
pointer	Σ	0..*	Reference	Pointer to next atomic sequence
structureVariant	Σ	0..*	BackboneElement	Structural variant
variantType	Σ	0..1	CodeableConcept	Structural variant change type LOINC LL379-9 answerlist (required)
exact	Σ	0..1	boolean	Does the structural variant have base pair resolution breakpoints?
length	Σ	0..1	integer	Structural variant length
outer	Σ	0..1	BackboneElement	Structural variant outer
start	Σ	0..1	integer	Structural variant outer start
end	Σ	0..1	integer	Structural variant outer end
inner	Σ	0..1	BackboneElement	Structural variant inner
start	Σ	0..1	integer	Structural variant inner start
end	Σ	0..1	integer	Structural variant inner end