> ## Documentation Index > Fetch the complete documentation index at: https://docs.metriport.com/llms.txt > Use this file to discover all available pages before exploring further. # MolecularSequence > Raw data describing a biological sequence. ## Properties | Name | Required | Type | Description | | --------------------- | -------- | --------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | identifier | No | [Identifier](/medical-api/fhir/data-types/identifier)\[] | Unique ID for this particular sequence. This is a FHIR-defined id | | type | No | code | aa / dna / rna | | coordinateSystem | Yes | 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 | No | Reference\<[Patient](/medical-api/fhir/resources/patient)> | Who and/or what this is about | | specimen | No | Reference\<[Specimen](/medical-api/fhir/resources/specimen)> | Specimen used for sequencing | | device | No | Reference\<[Device](/medical-api/fhir/resources/device)> | The method for sequencing | | performer | No | Reference\<[Organization](/medical-api/fhir/resources/organization)> | Who should be responsible for test result | | quantity | No | [Quantity](/medical-api/fhir/data-types/quantity) | The number of copies of the sequence of interest. (RNASeq) | | referenceSeq | No | MolecularSequenceReferenceSeq | A sequence used as reference | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - chromosome | No | [CodeableConcept](/medical-api/fhir/data-types/codeableconcept) | Chromosome containing genetic finding | | - genomeBuild | No | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' | | - orientation | No | code | sense / antisense | | - referenceSeqId | No | [CodeableConcept](/medical-api/fhir/data-types/codeableconcept) | Reference identifier | | - referenceSeqPointer | No | Reference\<[MolecularSequence](/medical-api/fhir/resources/molecularsequence)> | A pointer to another MolecularSequence entity as reference sequence | | - referenceSeqString | No | string | A string to represent reference sequence | | - strand | No | code | watson / crick | | - windowStart | No | integer | Start position of the window on the reference sequence | | - windowEnd | No | integer | End position of the window on the reference sequence | | variant | No | MolecularSequenceVariant | Variant in sequence | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - start | No | integer | Start position of the variant on the reference sequence | | - end | No | integer | End position of the variant on the reference sequence | | - observedAllele | No | string | Allele that was observed | | - referenceAllele | No | string | Allele in the reference sequence | | - cigar | No | string | Extended CIGAR string for aligning the sequence with reference bases | | - variantPointer | No | Reference\<[Observation](/medical-api/fhir/resources/observation)> | Pointer to observed variant information | | observedSeq | No | string | Sequence that was observed | | quality | No | MolecularSequenceQuality | An set of value as quality of sequence | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - type | Yes | code | indel / snp / unknown | | - standardSequence | No | [CodeableConcept](/medical-api/fhir/data-types/codeableconcept) | Standard sequence for comparison | | - start | No | integer | Start position of the sequence | | - end | No | integer | End position of the sequence | | - score | No | [Quantity](/medical-api/fhir/data-types/quantity) | Quality score for the comparison | | - method | No | [CodeableConcept](/medical-api/fhir/data-types/codeableconcept) | Method to get quality | | - truthTP | No | decimal | True positives from the perspective of the truth data | | - queryTP | No | decimal | True positives from the perspective of the query data | | - truthFN | No | decimal | False negatives | | - queryFP | No | decimal | False positives | | - gtFP | No | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match | | - precision | No | decimal | Precision of comparison | | - recall | No | decimal | Recall of comparison | | - fScore | No | decimal | F-score | | - roc | No | MolecularSequenceQualityRoc | Receiver Operator Characteristic (ROC) Curve | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - score | No | integer\[] | Genotype quality score | | - numTP | No | integer\[] | Roc score true positive numbers | | - numFP | No | integer\[] | Roc score false positive numbers | | - numFN | No | integer\[] | Roc score false negative numbers | | - precision | No | decimal\[] | Precision of the GQ score | | - sensitivity | No | decimal\[] | Sensitivity of the GQ score | | - fMeasure | No | decimal\[] | FScore of the GQ score | | readCoverage | No | integer | Average number of reads representing a given nucleotide in the reconstructed sequence | | repository | No | MolecularSequenceRepository | External repository which contains detailed report related with observedSeq in this resource | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - type | Yes | code | directlink / openapi / login / oauth / other | | - url | No | uri | URI of the repository | | - name | No | string | Repository's name | | - datasetId | No | string | Id of the dataset that used to call for dataset in repository | | - variantsetId | No | string | Id of the variantset that used to call for variantset in repository | | - readsetId | No | string | Id of the read | | pointer | No | Reference\<[MolecularSequence](/medical-api/fhir/resources/molecularsequence)>\[] | Pointer to next atomic sequence | | structureVariant | No | MolecularSequenceStructureVariant | Structural variant | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - variantType | No | [CodeableConcept](/medical-api/fhir/data-types/codeableconcept) | Structural variant change type | | - exact | No | boolean | Does the structural variant have base pair resolution breakpoints? | | - length | No | integer | Structural variant length | | - outer | No | MolecularSequenceStructureVariantOuter | Structural variant outer | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - start | No | integer | Structural variant outer start | | - end | No | integer | Structural variant outer end | | - inner | No | MolecularSequenceStructureVariantInner | Structural variant inner | | - id | No | string | Unique id for inter-element referencing | | - extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | - modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored even if unrecognized | | - start | No | integer | Structural variant inner start | | - end | No | integer | Structural variant inner end | ## Search Parameters | Name | Type | Description | Expression | | --------------------------------- | --------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------- | | chromosome | token | Chromosome number of the reference sequence | MolecularSequence.referenceSeq.chromosome | | identifier | token | The unique identity for a particular sequence | MolecularSequence.identifier | | patient | reference | The subject that the observation is about | MolecularSequence.patient | | referenceseqid | token | Reference Sequence of the sequence | MolecularSequence.referenceSeq.referenceSeqId | | type | token | Amino Acid Sequence/ DNA Sequence / RNA Sequence | MolecularSequence.type | | variant-end | number | End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant. | MolecularSequence.variant.end | | variant-start | number | Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant. | MolecularSequence.variant.start | | window-end | number | End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence. | MolecularSequence.referenceSeq.windowEnd | | window-start | number | Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence. | MolecularSequence.referenceSeq.windowStart | | chromosome-variant-coordinate | composite | Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and \<345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | MolecularSequence.variant | | chromosome-window-coordinate | composite | Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and \<345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | MolecularSequence.referenceSeq | | referenceseqid-variant-coordinate | composite | Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC\_000001.11 and with position >123 and \<345, where in 1-based system resource, all strings within region NC\_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC\_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | MolecularSequence.variant | | referenceseqid-window-coordinate | composite | Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC\_000001.11 and with position >123 and \<345, where in 1-based system resource, all strings within region NC\_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC\_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | MolecularSequence.referenceSeq | ## Inherited Properties | Name | Required | Type | Description | | ----------------- | -------- | ------------------------------------------------------ | ------------------------------------------------------ | | id | No | string | Logical id of this artifact | | meta | No | [Meta](/medical-api/fhir/data-types/meta) | Metadata about the resource | | implicitRules | No | uri | A set of rules under which this content was created | | language | No | code | Language of the resource content | | text | No | [Narrative](/medical-api/fhir/data-types/narrative) | Text summary of the resource, for human interpretation | | contained | No | Resource\[] | Contained, inline Resources | | extension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Additional content defined by implementations | | modifierExtension | No | [Extension](/medical-api/fhir/data-types/extension)\[] | Extensions that cannot be ignored | To view the FHIR specification for this resource, see [MolecularSequence](https://www.hl7.org/fhir/StructureDefinition/MolecularSequence).