| Name | Flags | Card. | Type | Description & Constraints![]() |
|---|---|---|---|---|
| ΣI | DomainResource | Information about a biological sequence Only 0 and 1 are valid for coordinateSystem | ||
| Σ | 0..* | Identifier | Unique ID for this particular sequence. This is a FHIR-defined id | |
| Σ | 0..1 | code | AA | DNA | RNA sequenceType (Example) | |
| 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) | |
| Σ | 0..1 | Reference(Patient) | Who and/or what this is about | |
| Σ | 0..1 | Reference(Specimen) | Specimen used for sequencing | |
| Σ | 0..1 | Reference(Device) | The method for sequencing | |
| Σ | 0..1 | Reference(Organization) | Who should be responsible for test result | |
| Σ | 0..1 | Quantity | The number of copies of the seqeunce of interest. (RNASeq) | |
| ΣI | 0..1 | BackboneElement | Reference sequence Only +1 and -1 are valid for strand GenomeBuild and chromosome must be both contained if either one of them is contained Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; | |
| Σ | 0..1 | CodeableConcept | Chromosome containing genetic finding chromosome-human (Example) | |
| Σ | 0..1 | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' | |
| Σ | 0..1 | CodeableConcept | Reference identifier ENSEMBL (Example) | |
| Σ | 0..1 | Reference(Sequence) | A Pointer to another Sequence entity as reference sequence | |
| Σ | 0..1 | string | A Reference Sequence string | |
| Σ | 0..1 | integer | Directionality of DNA ( +1/-1) | |
| Σ | 1..1 | integer | Start position of the window on the reference sequence | |
| Σ | 1..1 | integer | End position of the window on the reference sequence | |
| Σ | 0..* | BackboneElement | Sequence variant | |
| Σ | 0..1 | integer | Start position of the variant on the reference sequence | |
| Σ | 0..1 | integer | End position of the variant on the reference sequence | |
| Σ | 0..1 | string | Allele that was observed | |
| Σ | 0..1 | string | Allele of reference sequence | |
| Σ | 0..1 | string | Extended CIGAR string for aligning the sequence with reference bases | |
| Σ | 0..1 | Reference(Observation) | Pointer to observed variant information | |
| Σ | 0..1 | string | Observed sequence | |
| Σ | 0..* | BackboneElement | Sequence quality | |
| Σ | 1..1 | code | INDEL | SNP | UNKNOWN qualityType (Required) | |
| Σ | 0..1 | CodeableConcept | Standard sequence for comparison | |
| Σ | 0..1 | integer | Start position of the sequence | |
| Σ | 0..1 | integer | End position of the sequence | |
| Σ | 0..1 | Quantity | Quality score | |
| Σ | 0..1 | CodeableConcept | Method for quality | |
| Σ | 0..1 | decimal | True positives from the perspective of the truth data | |
| Σ | 0..1 | decimal | True positives from the perspective of the query data | |
| Σ | 0..1 | decimal | False negatives | |
| Σ | 0..1 | decimal | False positives | |
| Σ | 0..1 | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match | |
| Σ | 0..1 | decimal | Precision | |
| Σ | 0..1 | decimal | Recall | |
| Σ | 0..1 | decimal | F-score | |
| Σ | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence | |
| Σ | 0..* | BackboneElement | External repository which contains detailed report related with observedSeq in this resource | |
| Σ | 1..1 | code | directlink | openapi | login | oauth | other repositoryType (Required) | |
| Σ | 0..1 | uri | URI of the repository | |
| Σ | 0..1 | string | Name of the repository | |
| Σ | 0..1 | string | Id of the dataset that used to call for dataset in repository | |
| Σ | 0..1 | string | Id of the variantset that used to call for variantset in repository | |
| Σ | 0..1 | string | Id of the read | |
| Σ | 0..* | Reference(Sequence) | Pointer to next atomic sequence | |
| Σ | 0..* | BackboneElement | Structural variant | |
| Σ | 0..1 | string | Precision of boundaries | |
| Σ | 0..1 | decimal | Structural Variant reported aCGH ratio | |
| Σ | 0..1 | integer | Structural Variant Length | |
| Σ | 0..1 | BackboneElement | Structural variant outer | |
| Σ | 0..1 | integer | Structural Variant Outer Start | |
| Σ | 0..1 | integer | Structural Variant Outer End | |
| Σ | 0..1 | BackboneElement | Structural variant inner | |
| Σ | 0..1 | integer | Structural Variant Inner Start | |
| Σ | 0..1 | integer | Structural Variant Inner End | |
Documentation for this format | ||||