Generated Narrative: StructureDefinition profile-MolecularSequence Name Flags Card. Type Description & Constraints MolecularSequence 0..* MolecularSequence(4.0.1) Information about a biological sequence #xD; Slices for extension 1..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:focus 0..* Reference(Cross-version Profile for R5.Resource for use in FHIR R4(0.1.0) | Resource) R5: What the molecular sequence is about, when it is not about the subject of record (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus #xD; extension:formatted 0..* Attachment R5: Embedded file or a link (URL) which contains content to represent the sequence (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted #xD; extension:coordinateSystem 1..1 CodeableConcept R5: Ways of identifying nucleotides or amino acids within a sequence (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem #xD; extension:ordinalPosition 0..1 integer R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition #xD; extension:sequenceRange 0..1 Range R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange #xD; patient #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:subject 0..1 Reference(Resource) R5: Subject this sequence is associated too URL: http://hl7.org/fhir/StructureDefinition/alternate-reference #xD; referenceSeq #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:genomeAssembly 0..1 CodeableConcept R5: The genome assembly used for starting sequence, e.g. GRCh38 (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly #xD; extension:sequence 0..1 CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR R4(0.1.0) | MolecularSequence) R5: The reference sequence that represents the starting sequence additional types URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence #xD; chromosome #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:chromosome 0..1 CodeableConcept R5: Chromosome Identifier URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome #xD; variant #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:start 0..1 integer R5: Start position of the edit on the starting sequence (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start #xD; Documentation for this format
Cross-version Profile for R5.MolecularSequence for use in FHIR R4
This cross-version profile allows R5 MolecularSequence content to be represented via FHIR R4 MolecularSequence resources.
Raw data describing a biological sequence.
If the resource is contained in another resource, it SHALL NOT contain nested Resources
not(parent::f:contained and f:contained)
If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))
If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))
If a resource is contained in another resource, it SHALL NOT have a security label
When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time.
A resource should have narrative for robust management
Only 0 and 1 are valid for coordinateSystem
coordinateSystem = 1 or coordinateSystem = 0
count(f:coordinateSystem[@value=0 and @value=1]) = 1
The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
The only time that a resource does not have an id is when it is being submitted to the server using a create operation.
The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
A set of rules under which this content was created
A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.
Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.
This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation
The base language in which the resource is written.
Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).
Text summary of the resource, for human interpretation
A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.
Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.
These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.
This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
R5: What the molecular sequence is about, when it is not about the subject of record (new)
R5: `MolecularSequence.focus` (new:Reference(Resource))
Element `MolecularSequence.focus` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`. Element `MolecularSequence.focus` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).
exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])
R5: Embedded file or a link (URL) which contains content to represent the sequence (new)
R5: `MolecularSequence.formatted` (new:Attachment)
Element `MolecularSequence.formatted` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`. Element `MolecularSequence.formatted` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).
R5: Ways of identifying nucleotides or amino acids within a sequence (new)
R5: `MolecularSequence.relative.coordinateSystem` (new:CodeableConcept)
Element `MolecularSequence.relative.coordinateSystem` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`. Element `MolecularSequence.relative.coordinateSystem` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).
R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)
R5: `MolecularSequence.relative.ordinalPosition` (new:integer)
Element `MolecularSequence.relative.ordinalPosition` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`. Element `MolecularSequence.relative.ordinalPosition` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).
R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)
R5: `MolecularSequence.relative.sequenceRange` (new:Range)
Element `MolecularSequence.relative.sequenceRange` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`. Element `MolecularSequence.relative.sequenceRange` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).
May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Unique ID for this particular sequence. This is a FHIR-defined id
A unique identifier for this particular sequence instance. This is a FHIR-defined id.
Allows sequences to be distinguished and referenced.
Amino Acid Sequence/ DNA Sequence / RNA Sequence.
Type if a sequence -- DNA, RNA, or amino acid sequence.
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)
Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).
The patient whose sequencing results are described by this resource.
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
R5: Subject this sequence is associated too
Element `MolecularSequence.subject` is mapped to FHIR R4 element `MolecularSequence.patient` as `SourceIsBroaderThanTarget`. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.subject` with unmapped reference targets: BiologicallyDerivedProduct, Group, NutritionProduct, Substance.
Literal reference, Relative, internal or absolute URL
A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.
Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server.
Type the reference refers to (e.g. "Patient")
The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent. The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).
This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.
Aa resource (or, for logical models, the URI of the logical model).
Logical reference, when literal reference is not known
An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.
When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).
Plain text narrative that identifies the resource in addition to the resource reference.
This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.
The method for sequencing, for example, chip information.
Who should be responsible for test result
The organization or lab that should be responsible for this result.
The number of copies of the sequence of interest. (RNASeq)
The number of copies of the sequence of interest. (RNASeq).
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
GenomeBuild and chromosome must be both contained if either one of them is contained
(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())
(exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild)))
Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1
R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)
R5: `MolecularSequence.relative.startingSequence.genomeAssembly` (new:CodeableConcept)
Element `MolecularSequence.relative.startingSequence.genomeAssembly` has a context of MolecularSequence.referenceSeq based on following the parent source element upwards and mapping to `MolecularSequence`. Element `MolecularSequence.relative.startingSequence.genomeAssembly` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).
R5: The reference sequence that represents the starting sequence additional types
R5: `MolecularSequence.relative.startingSequence.sequence[x]` additional types (CodeableConcept, Reference(http://hl7.org/fhir/StructureDefinition/MolecularSequence))
Element `MolecularSequence.relative.startingSequence.sequence[x]` is mapped to FHIR R4 element `MolecularSequence.referenceSeq.referenceSeqString` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.relative.startingSequence.sequence[x]` do not cover the following types: CodeableConcept, Reference. A starting sequence may be represented in one of three ways: 1. CodeableConcept, using NCBI, LRG or other appropriate code systems 1. a simple string of IUPAC codes 1. a reference to another MolecularSequence resource.
Extensions that cannot be ignored even if unrecognized
May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).
R5: `MolecularSequence.relative.startingSequence.chromosome`
Element `MolecularSequence.relative.startingSequence.chromosome` is mapped to FHIR R4 element `MolecularSequence.referenceSeq.chromosome` as `Equivalent`.
A reference to a code defined by a terminology system.
Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.
Allows for alternative encodings within a code system, and translations to other code systems.
fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding
Plain text representation of the concept
A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.
Very often the text is the same as a displayName of one of the codings.
The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.
C*E.9. But note many systems use C*E.2 for this
fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText
The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.
A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.
Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.
A pointer to another MolecularSequence entity as reference sequence
A pointer to another MolecularSequence entity as reference sequence.
A string to represent reference sequence
An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.
Start position of the window on the reference sequence
Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
End position of the window on the reference sequence
End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.
R5: Start position of the edit on the starting sequence (new)
R5: `MolecularSequence.relative.edit.start` (new:integer)
Element `MolecularSequence.relative.edit.start` has a context of MolecularSequence.variant based on following the parent source element upwards and mapping to `MolecularSequence`. Element `MolecularSequence.relative.edit.start` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).
Start position of the variant on the reference sequence
Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
End position of the variant on the reference sequence
End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
Extended CIGAR string for aligning the sequence with reference bases
Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
A pointer to an Observation containing variant information.
Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
Additional content defined by implementations
May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
Gold standard sequence used for comparing against.
Reference identifier of the sequence that used to mark the quality of tested samples.
Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
Which method is used to get sequence quality.
The method used to evaluate the numerical quality of the observed sequence.
True positives from the perspective of the truth data
True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
True positives from the perspective of the query data
True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.
False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.
False positives where the non-REF alleles in the Truth and Query Call Sets match
The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).
Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
Receiver Operator Characteristic (ROC) Curve
Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
Invidual data point representing the GQ (genotype quality) score threshold.
The number of true positives if the GQ score threshold was set to "score" field value.
The number of false positives if the GQ score threshold was set to "score" field value.
The number of false negatives if the GQ score threshold was set to "score" field value.
Calculated precision if the GQ score threshold was set to "score" field value.
Calculated sensitivity if the GQ score threshold was set to "score" field value.
Calculated fScore if the GQ score threshold was set to "score" field value.
Average number of reads representing a given nucleotide in the reconstructed sequence
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
External repository which contains detailed report related with observedSeq in this resource
Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
directlink | openapi | login | oauth | other
Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
URI of an external repository which contains further details about the genetics data.
Id of the dataset that used to call for dataset in repository
Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.
Id of the variantset that used to call for variantset in repository
Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.
Id of the read in this external repository.
Pointer to next atomic sequence which at most contains one variant.
Information about chromosome structure variation.
Information about chromosome structure variation DNA change type.
Does the structural variant have base pair resolution breakpoints?
Used to indicate if the outer and inner start-end values have the same meaning.
Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Structural variant outer end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Structural variant inner end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.