ext-R4B-MolecularSequence.quality
type: StructureDefinition
node role: treeRoot
id:
  v: ext-R4B-MolecularSequence.quality
text:
  status:
    v: extensions
  div: Generated Narrative: StructureDefinition ext-R4B-MolecularSequence.quality Name Flags Card. Type Description & Constraints<img src="[binary]" alt="doco" style="background-color: inherit"/> Extension 0..* Extension(5.0.0) An set of value as quality of sequence #xD; Slices for extension 1..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:type 1..1 Extension indel | snp | unknown #xD; url 1..1 uri "type" #xD; value[x] 0..1 code indel | snp | unknown Binding: R4B_quality_type_for_R5 (0.0.1-snapshot-2) (required): Type for quality #xD; extension:standardSequence 0..1 Extension Standard sequence for comparison #xD; url 1..1 uri "standardSequence" #xD; value[x] 0..1 CodeableConcept Standard sequence for comparison Binding: R4B_sequence_quality_standardSequence_for_R5 (0.0.1-snapshot-2) (example): Reference identifier for standard sequence #xD; extension:start 0..1 Extension Start position of the sequence #xD; url 1..1 uri "start" #xD; value[x] 0..1 integer Start position of the sequence #xD; extension:end 0..1 Extension End position of the sequence #xD; url 1..1 uri "end" #xD; value[x] 0..1 integer End position of the sequence #xD; extension:score 0..1 Extension Quality score for the comparison #xD; url 1..1 uri "score" #xD; value[x] 0..1 Quantity Quality score for the comparison #xD; extension:method 0..1 Extension Method to get quality #xD; url 1..1 uri "method" #xD; value[x] 0..1 CodeableConcept Method to get quality Binding: R4B_sequence_quality_method_for_R5 (0.0.1-snapshot-2) (example): How to get the numerical score #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.quality-definitions.html#Extension.extension:truthTP" title="Slice truthTP: 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.">extension:truthTP…
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      v: 0.0.1-snapshot-2
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      value: canonical
        v: http://hl7.org/fhir/4.3/ImplementationGuide/hl7.fhir.uv.xver-r4b.r5
        link: http://hl7.org/fhir/4.3/ImplementationGuide/hl7.fhir.uv.xver-r4b.r5
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        link: http://hl7.org/fhir/4.3/ImplementationGuide/hl7.fhir.uv.xver-r4b.r5
url:
  v: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.quality
version:
  v: 0.0.1-snapshot-2
name:
  v: Ext_R4B_MolecularSequence_quality
title:
  v: Cross-version Extension for R4B.MolecularSequence.quality for use in FHIR R5
status:
  v: active
experimental:
  v: false
date:
  v: 2025-09-01T22:36:53.38042+10:00
publisher:
  v: FHIR Infrastructure
contact:
  name:
    v: FHIR Infrastructure
  telecom:
    system:
      v: url
    value:
      v: http://www.hl7.org/Special/committees/fiwg
description:
  v: This cross-version extension represents MolecularSequence.quality from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0 for use in FHIR R5.
jurisdiction:
  coding:
    system:
      v: http://unstats.un.org/unsd/methods/m49/m49.htm
    code:
      v: 001
    display:
      v: World
fhir version:
  v: 5.0.0
mapping:
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  name:
    v: RIM Mapping
kind:
  v: complex-type
abstract:
  v: false
context:
  type:
    v: element
  expression:
    v: MolecularSequence
type:
  v: Extension
base definition:
  v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
  link: 5.0
  link: .0
derivation:
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    path:
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    short:
      v: An set of value as quality of sequence
    definition:
      v: 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)).
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comment:
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id:
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path:
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path:
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slice name:
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id:
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  v: Unique id for inter-element referencing
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  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
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comment:
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path:
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id:
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path:
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definition:
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definition:
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comment:
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alias:
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  v: Start position of the sequence
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comment:
  v: 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.
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  v: identifies the meaning of the extension
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  identity:
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    v: N/A

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  v: End position of the sequence
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  v: Unique id for inter-element referencing
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  v: identifies the meaning of the extension
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    v: All FHIR elements must have a @value or children
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id:
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path:
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binding:
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id:
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path:
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slice name:
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short:
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definition:
  v: 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.
comment:
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id:
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  v: Unique id for inter-element referencing
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  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
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    value: url
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mapping:
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    v: n/a

id:
  v: Extension.extension:truthTP.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:truthTP.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: truthTP
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:truthTP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: True positives from the perspective of the truth data
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:queryTP
path:
  v: Extension.extension
slice name:
  v: queryTP
short:
  v: True positives from the perspective of the query data
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

id:
  v: Extension.extension:queryTP.id
path:
  v: Extension.extension.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: id
  code:
    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:queryTP.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:queryTP.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: queryTP
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:queryTP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: True positives from the perspective of the query data
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:truthFN
path:
  v: Extension.extension
slice name:
  v: truthFN
short:
  v: False negatives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

id:
  v: Extension.extension:truthFN.id
path:
  v: Extension.extension.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: id
  code:
    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:truthFN.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:truthFN.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: truthFN
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:truthFN.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: False negatives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:queryFP
path:
  v: Extension.extension
slice name:
  v: queryFP
short:
  v: False positives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

id:
  v: Extension.extension:queryFP.id
path:
  v: Extension.extension.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: id
  code:
    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:queryFP.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:queryFP.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: queryFP
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:queryFP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: False positives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:gtFP
path:
  v: Extension.extension
slice name:
  v: gtFP
short:
  v: False positives where the non-REF alleles in the Truth and Query Call Sets match
definition:
  v: 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).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

id:
  v: Extension.extension:gtFP.id
path:
  v: Extension.extension.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: id
  code:
    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:gtFP.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:gtFP.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: gtFP
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:gtFP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: False positives where the non-REF alleles in the Truth and Query Call Sets match
definition:
  v: 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).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:precision
path:
  v: Extension.extension
slice name:
  v: precision
short:
  v: Precision of comparison
definition:
  v: QUERY.TP / (QUERY.TP + QUERY.FP).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

id:
  v: Extension.extension:precision.id
path:
  v: Extension.extension.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: id
  code:
    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:precision.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:precision.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: precision
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:precision.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: Precision of comparison
definition:
  v: QUERY.TP / (QUERY.TP + QUERY.FP).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:recall
path:
  v: Extension.extension
slice name:
  v: recall
short:
  v: Recall of comparison
definition:
  v: TRUTH.TP / (TRUTH.TP + TRUTH.FN).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

id:
  v: Extension.extension:recall.id
path:
  v: Extension.extension.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: id
  code:
    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:recall.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:recall.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: recall
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:recall.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: Recall of comparison
definition:
  v: TRUTH.TP / (TRUTH.TP + TRUTH.FN).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:fScore
path:
  v: Extension.extension
slice name:
  v: fScore
short:
  v: F-score
definition:
  v: Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

id:
  v: Extension.extension:fScore.id
path:
  v: Extension.extension.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: id
  code:
    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:fScore.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  description:
    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: Extension.extension:fScore.url
path:
  v: Extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: fScore
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:fScore.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: F-score
definition:
  v: Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc
path:
  v: Extension.extension
slice name:
  v: roc
short:
  v: Receiver Operator Characteristic (ROC) Curve
definition:
  v: Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
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comment:
  v: 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.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
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  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
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mapping:
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  map:
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id:
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path:
  v: Extension.extension.extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
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  extension:
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    value: url
      v: uri
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    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: numFN
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  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc.extension:numFN.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Roc score false negative numbers
definition:
  v: The number of false negatives if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
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  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
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    v: 0
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    v: 1
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  code:
    v: integer
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  v: ext-1
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  key:
    v: ele-1
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    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
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path:
  v: Extension.extension.extension
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  v: precision
short:
  v: Precision of the GQ score
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  v: Calculated precision if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
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  v: 0
max:
  v: *
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  path:
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    v: 0
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    v: *
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  code:
    v: Extension
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  key:
    v: ele-1
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    v: error
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    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
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  key:
    v: ext-1
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    v: Must have either extensions or value[x], not both
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    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
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  v: false

id:
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path:
  v: Extension.extension.extension.id
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  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
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    v: 1
type:
  extension:
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    value: url
      v: id
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    v: http://hl7.org/fhirpath/System.String
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  v: ele-1
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  v: false
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  identity:
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  map:
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id:
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      v: value
    path:
      v: url
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    v: Extensions are always sliced by (at least) url
  rules:
    v: open
short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
  v: extensions
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  v: user content
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  v: 0
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  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
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    v: *
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  code:
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  key:
    v: ele-1
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  human:
    v: All FHIR elements must have a @value or children
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    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
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    v: error
  human:
    v: Must have either extensions or value[x], not both
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    v: extension.exists() != value.exists()
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    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
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mapping:
  identity:
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  map:
    v: n/a

id:
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  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
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  v: 1
base:
  path:
    v: Extension.url
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    v: 1
  max:
    v: 1
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  extension:
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    value: url
      v: uri
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    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: precision
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc.extension:precision.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Precision of the GQ score
definition:
  v: Calculated precision if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
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    v: 1
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  code:
    v: decimal
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  v: ext-1
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  key:
    v: ele-1
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    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
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    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc.extension:sensitivity
path:
  v: Extension.extension.extension
slice name:
  v: sensitivity
short:
  v: Sensitivity of the GQ score
definition:
  v: Calculated sensitivity if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
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  v: 0
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  v: *
base:
  path:
    v: Element.extension
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    v: 0
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    v: *
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  key:
    v: ele-1
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    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
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  key:
    v: ext-1
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    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
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    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
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is summary:
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id:
  v: Extension.extension:roc.extension:sensitivity.id
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  v: xmlAttr
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  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
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  v: 1
base:
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    value: url
      v: id
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    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
is modifier:
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is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
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  v: Extension.extension.extension.extension
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  discriminator:
    type:
      v: value
    path:
      v: url
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    v: Extensions are always sliced by (at least) url
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    v: open
short:
  v: Additional content defined by implementations
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  v: 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 managable, 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.
comment:
  v: 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.
alias:
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  v: *
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    link: .0
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    v: ext-1
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    v: error
  human:
    v: Must have either extensions or value[x], not both
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    link: .0
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  map:
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id:
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representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
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    v: 1
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    v: 1
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  extension:
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    value: url
      v: uri
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    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: sensitivity
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  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc.extension:sensitivity.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Sensitivity of the GQ score
definition:
  v: Calculated sensitivity if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
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    v: 0
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    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
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  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc.extension:fMeasure
path:
  v: Extension.extension.extension
slice name:
  v: fMeasure
short:
  v: FScore of the GQ score
definition:
  v: Calculated fScore if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
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  v: 0
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  v: *
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    v: Extension
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    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
constraint:
  key:
    v: ext-1
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    v: error
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    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
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    v: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
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is summary:
  v: false

id:
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  v: xmlAttr
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  v: Unique id for inter-element referencing
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  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
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  v: 0
max:
  v: 1
base:
  path:
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    v: 0
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    v: 1
type:
  extension:
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    value: url
      v: id
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    v: http://hl7.org/fhirpath/System.String
condition:
  v: ele-1
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is summary:
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  identity:
    v: rim
  map:
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id:
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      v: value
    path:
      v: url
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    v: Extensions are always sliced by (at least) url
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short:
  v: Additional content defined by implementations
definition:
  v: 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 managable, 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.
comment:
  v: 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.
alias:
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alias:
  v: user content
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  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
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    v: 0
  max:
    v: *
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  code:
    v: Extension
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  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
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    v: Must have either extensions or value[x], not both
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  map:
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id:
  v: Extension.extension:roc.extension:fMeasure.url
path:
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representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
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base:
  path:
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    v: 1
  max:
    v: 1
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  extension:
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    value: url
      v: uri
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    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: fMeasure
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  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc.extension:fMeasure.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: FScore of the GQ score
definition:
  v: Calculated fScore if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
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    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.extension:roc.url
path:
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representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
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max:
  v: 1
base:
  path:
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    v: 1
  max:
    v: 1
type:
  extension:
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    value: url
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    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: roc
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  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
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path:
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short:
  v: Value of extension
definition:
  v: Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).
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base:
  path:
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    v: 0
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    v: 1
type:
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    v: base64Binary
type:
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    v: boolean
type:
  code:
    v: canonical
type:
  code:
    v: code
type:
  code:
    v: date
type:
  code:
    v: dateTime
type:
  code:
    v: decimal
type:
  code:
    v: id
type:
  code:
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type:
  code:
    v: integer
type:
  code:
    v: integer64
type:
  code:
    v: markdown
type:
  code:
    v: oid
type:
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    v: positiveInt
type:
  code:
    v: string
type:
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    v: time
type:
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    v: unsignedInt
type:
  code:
    v: uri
type:
  code:
    v: url
type:
  code:
    v: uuid
type:
  code:
    v: Address
type:
  code:
    v: Age
type:
  code:
    v: Annotation
type:
  code:
    v: Attachment
type:
  code:
    v: CodeableConcept
type:
  code:
    v: CodeableReference
type:
  code:
    v: Coding
type:
  code:
    v: ContactPoint
type:
  code:
    v: Count
type:
  code:
    v: Distance
type:
  code:
    v: Duration
type:
  code:
    v: HumanName
type:
  code:
    v: Identifier
type:
  code:
    v: Money
type:
  code:
    v: Period
type:
  code:
    v: Quantity
type:
  code:
    v: Range
type:
  code:
    v: Ratio
type:
  code:
    v: RatioRange
type:
  code:
    v: Reference
type:
  code:
    v: SampledData
type:
  code:
    v: Signature
type:
  code:
    v: Timing
type:
  code:
    v: ContactDetail
type:
  code:
    v: DataRequirement
type:
  code:
    v: Expression
type:
  code:
    v: ParameterDefinition
type:
  code:
    v: RelatedArtifact
type:
  code:
    v: TriggerDefinition
type:
  code:
    v: UsageContext
type:
  code:
    v: Availability
type:
  code:
    v: ExtendedContactDetail
type:
  code:
    v: Dosage
type:
  code:
    v: Meta
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

identity:
  v: rim
map:
  v: N/A

id:
  v: Extension.url
path:
  v: Extension.url
representation:
  v: xmlAttr
short:
  v: identifies the meaning of the extension
definition:
  v: Source of the definition for the extension code - a logical name or a URL.
comment:
  v: The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: uri
  code:
    v: http://hl7.org/fhirpath/System.String
fixed: uri
  v: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.quality
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: Extension.value[x]
path:
  v: Extension.value[x]
short:
  v: Value of extension
definition:
  v: Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
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type:
  code:
    v: base64Binary
type:
  code:
    v: boolean
type:
  code:
    v: canonical
type:
  code:
    v: code
type:
  code:
    v: date
type:
  code:
    v: dateTime
type:
  code:
    v: decimal
type:
  code:
    v: id
type:
  code:
    v: instant
type:
  code:
    v: integer
type:
  code:
    v: integer64
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    v: string
type:
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    v: unsignedInt
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  code:
    v: uri
type:
  code:
    v: url
type:
  code:
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type:
  code:
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type:
  code:
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  code:
    v: Annotation
type:
  code:
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type:
  code:
    v: CodeableReference
type:
  code:
    v: Coding
type:
  code:
    v: ContactPoint
type:
  code:
    v: Count
type:
  code:
    v: Distance
type:
  code:
    v: Duration
type:
  code:
    v: HumanName
type:
  code:
    v: Identifier
type:
  code:
    v: Money
type:
  code:
    v: Period
type:
  code:
    v: Quantity
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  code:
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  code:
    v: SampledData
type:
  code:
    v: Signature
type:
  code:
    v: Timing
type:
  code:
    v: ContactDetail
type:
  code:
    v: DataRequirement
type:
  code:
    v: Expression
type:
  code:
    v: ParameterDefinition
type:
  code:
    v: RelatedArtifact
type:
  code:
    v: TriggerDefinition
type:
  code:
    v: UsageContext
type:
  code:
    v: Availability
type:
  code:
    v: ExtendedContactDetail
type:
  code:
    v: Dosage
type:
  code:
    v: Meta
condition:
  v: ext-1
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element|5.0.0
    link: 5.0
    link: .0
is modifier:
  v: false
is summary:
  v: false

identity:
  v: rim
map:
  v: N/A

element:
  id:
    v: Extension
  path:
    v: Extension
  short:
    v: An set of value as quality of sequence
  definition:
    v: 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)).
  comment:
    v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
  min:
    v: 0
  max:
    v: *
  base:
    path:
      v: Extension
    min:
      v: 0
    max:
      v: *
element:
  id:
    v: Extension.extension
  path:
    v: Extension.extension
  slicing:
    discriminator:
      type:
        v: value
      path:
        v: url
    ordered:
      v: false
    rules:
      v: closed
  min:
    v: 1
  max:
    v: *
  base:
    path:
      v: Extension.extension
    min:
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    max:
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element:
  id:
    v: Extension.extension:type
  path:
    v: Extension.extension
  slice name:
    v: type
  short:
    v: indel | snp | unknown
  definition:
    v: INDEL / SNP / Undefined variant.
  comment:
    v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
  min:
    v: 1
  max:
    v: 1
  base:
    path:
      v: Extension.extension
    min:
      v: 0
    max:
      v: *
element:
  id:
    v: Extension.extension:type.url
  path:
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  min:
    v: 1
  max:
    v: 1
  base:
    path:
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    min:
      v: 1
    max:
      v: 1
  fixed: uri
    v: type
element:
  id:
    v: Extension.extension:type.value[x]
  path:
    v: Extension.extension.value[x]
  short:
    v: indel | snp | unknown
  definition:
    v: INDEL / SNP / Undefined variant.
  comment:
    v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
  base:
    path:
      v: Extension.value[x]
    min:
      v: 0
    max:
      v: 1
  type:
    code:
      v: code
  binding:
    strength:
      v: required
    description:
      v: Type for quality
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      v: http://hl7.org/fhir/4.3/ValueSet/R4B-quality-type-for-R5|0.0.1-snapshot-2
      link: 4.3
      link: 0.0
      link: .1
element:
  id:
    v: Extension.extension:standardSequence
  path:
    v: Extension.extension
  slice name:
    v: standardSequence
  short:
    v: Standard sequence for comparison
  definition:
    v: Gold standard sequence used for comparing against.
  comment:
    v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
  min:
    v: 0
  max:
    v: 1
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element:
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    v: standardSequence
element:
  id:
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  path:
    v: Extension.extension.value[x]
  short:
    v: Standard sequence for comparison
  definition:
    v: Gold standard sequence used for comparing against.
  comment:
    v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
  base:
    path:
      v: Extension.value[x]
    min:
      v: 0
    max:
      v: 1
  type:
    code:
      v: CodeableConcept
  binding:
    strength:
      v: example
    description:
      v: Reference identifier for standard sequence
    value set:
      v: http://hl7.org/fhir/4.3/ValueSet/R4B-sequence-quality-standardSequence-for-R5|0.0.1-snapshot-2
      link: 4.3
      link: 0.0
      link: .1
element:
  id:
    v: Extension.extension:start
  path:
    v: Extension.extension
  slice name:
    v: start

v: Start position of the sequence

v: Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

v: `MolecularSequence.quality` has no related element in R5:MolecularSequence

v: 0

v: 1

path:
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max:
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id:
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path:
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max:
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base:
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  max:
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fixed: uri
  v: start

id:
  v: Extension.extension:start.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: Start position of the sequence
definition:
  v: Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer

id:
  v: Extension.extension:end
path:
  v: Extension.extension
slice name:
  v: end
short:
  v: End position of the sequence
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
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base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:end.url
path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
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    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: end

id:
  v: Extension.extension:end.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: End position of the sequence
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer

id:
  v: Extension.extension:score
path:
  v: Extension.extension
slice name:
  v: score
short:
  v: Quality score for the comparison
definition:
  v: The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
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path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
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    v: 1
  max:
    v: 1
fixed: uri
  v: score

id:
  v: Extension.extension:score.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: Quality score for the comparison
definition:
  v: The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Quantity

id:
  v: Extension.extension:method
path:
  v: Extension.extension
slice name:
  v: method
short:
  v: Method to get quality
definition:
  v: Which method is used to get sequence quality.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
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path:
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min:
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max:
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base:
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  min:
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  max:
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fixed: uri
  v: method

id:
  v: Extension.extension:method.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: Method to get quality
definition:
  v: Which method is used to get sequence quality.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: CodeableConcept
binding:
  strength:
    v: example
  description:
    v: How to get the numerical score
  value set:
    v: http://hl7.org/fhir/4.3/ValueSet/R4B-sequence-quality-method-for-R5|0.0.1-snapshot-2
    link: 4.3
    link: 0.0
    link: .1

id:
  v: Extension.extension:truthTP
path:
  v: Extension.extension
slice name:
  v: truthTP
short:
  v: True positives from the perspective of the truth data
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:truthTP.url
path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: truthTP

id:
  v: Extension.extension:truthTP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: True positives from the perspective of the truth data
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:queryTP
path:
  v: Extension.extension
slice name:
  v: queryTP
short:
  v: True positives from the perspective of the query data
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
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path:
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min:
  v: 1
max:
  v: 1
base:
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  min:
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  max:
    v: 1
fixed: uri
  v: queryTP

id:
  v: Extension.extension:queryTP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: True positives from the perspective of the query data
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:truthFN
path:
  v: Extension.extension
slice name:
  v: truthFN
short:
  v: False negatives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
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path:
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min:
  v: 1
max:
  v: 1
base:
  path:
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  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: truthFN

id:
  v: Extension.extension:truthFN.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: False negatives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:queryFP
path:
  v: Extension.extension
slice name:
  v: queryFP
short:
  v: False positives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
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path:
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min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: queryFP

id:
  v: Extension.extension:queryFP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: False positives
definition:
  v: 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.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:gtFP
path:
  v: Extension.extension
slice name:
  v: gtFP
short:
  v: False positives where the non-REF alleles in the Truth and Query Call Sets match
definition:
  v: 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).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:gtFP.url
path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: gtFP

id:
  v: Extension.extension:gtFP.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: False positives where the non-REF alleles in the Truth and Query Call Sets match
definition:
  v: 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).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:precision
path:
  v: Extension.extension
slice name:
  v: precision
short:
  v: Precision of comparison
definition:
  v: QUERY.TP / (QUERY.TP + QUERY.FP).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:precision.url
path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: precision

id:
  v: Extension.extension:precision.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: Precision of comparison
definition:
  v: QUERY.TP / (QUERY.TP + QUERY.FP).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:recall
path:
  v: Extension.extension
slice name:
  v: recall
short:
  v: Recall of comparison
definition:
  v: TRUTH.TP / (TRUTH.TP + TRUTH.FN).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:recall.url
path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: recall

id:
  v: Extension.extension:recall.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: Recall of comparison
definition:
  v: TRUTH.TP / (TRUTH.TP + TRUTH.FN).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:fScore
path:
  v: Extension.extension
slice name:
  v: fScore
short:
  v: F-score
definition:
  v: Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:fScore.url
path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: fScore

id:
  v: Extension.extension:fScore.value[x]
path:
  v: Extension.extension.value[x]
short:
  v: F-score
definition:
  v: Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:roc
path:
  v: Extension.extension
slice name:
  v: roc
short:
  v: Receiver Operator Characteristic (ROC) Curve
definition:
  v: Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension
path:
  v: Extension.extension.extension
slicing:
  discriminator:
    type:
      v: value
    path:
      v: url
  ordered:
    v: false
  rules:
    v: closed
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:score
path:
  v: Extension.extension.extension
slice name:
  v: score
short:
  v: Genotype quality score
definition:
  v: Invidual data point representing the GQ (genotype quality) score threshold.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:score.url
path:
  v: Extension.extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: score

id:
  v: Extension.extension:roc.extension:score.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Genotype quality score
definition:
  v: Invidual data point representing the GQ (genotype quality) score threshold.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer

id:
  v: Extension.extension:roc.extension:numTP
path:
  v: Extension.extension.extension
slice name:
  v: numTP
short:
  v: Roc score true positive numbers
definition:
  v: The number of true positives if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:numTP.url
path:
  v: Extension.extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: numTP

id:
  v: Extension.extension:roc.extension:numTP.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Roc score true positive numbers
definition:
  v: The number of true positives if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer

id:
  v: Extension.extension:roc.extension:numFP
path:
  v: Extension.extension.extension
slice name:
  v: numFP
short:
  v: Roc score false positive numbers
definition:
  v: The number of false positives if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:numFP.url
path:
  v: Extension.extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: numFP

id:
  v: Extension.extension:roc.extension:numFP.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Roc score false positive numbers
definition:
  v: The number of false positives if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer

id:
  v: Extension.extension:roc.extension:numFN
path:
  v: Extension.extension.extension
slice name:
  v: numFN
short:
  v: Roc score false negative numbers
definition:
  v: The number of false negatives if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:numFN.url
path:
  v: Extension.extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: numFN

id:
  v: Extension.extension:roc.extension:numFN.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Roc score false negative numbers
definition:
  v: The number of false negatives if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer

id:
  v: Extension.extension:roc.extension:precision
path:
  v: Extension.extension.extension
slice name:
  v: precision
short:
  v: Precision of the GQ score
definition:
  v: Calculated precision if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:precision.url
path:
  v: Extension.extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: precision

id:
  v: Extension.extension:roc.extension:precision.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Precision of the GQ score
definition:
  v: Calculated precision if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:roc.extension:sensitivity
path:
  v: Extension.extension.extension
slice name:
  v: sensitivity
short:
  v: Sensitivity of the GQ score
definition:
  v: Calculated sensitivity if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:sensitivity.url
path:
  v: Extension.extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: sensitivity

id:
  v: Extension.extension:roc.extension:sensitivity.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: Sensitivity of the GQ score
definition:
  v: Calculated sensitivity if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:roc.extension:fMeasure
path:
  v: Extension.extension.extension
slice name:
  v: fMeasure
short:
  v: FScore of the GQ score
definition:
  v: Calculated fScore if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
min:
  v: 0
max:
  v: *
base:
  path:
    v: Extension.extension
  min:
    v: 0
  max:
    v: *

id:
  v: Extension.extension:roc.extension:fMeasure.url
path:
  v: Extension.extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: fMeasure

id:
  v: Extension.extension:roc.extension:fMeasure.value[x]
path:
  v: Extension.extension.extension.value[x]
short:
  v: FScore of the GQ score
definition:
  v: Calculated fScore if the GQ score threshold was set to "score" field value.
comment:
  v: `MolecularSequence.quality` has no related element in R5:MolecularSequence
base:
  path:
    v: Extension.value[x]
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal

id:
  v: Extension.extension:roc.url
path:
  v: Extension.extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: roc

id:
  v: Extension.url
path:
  v: Extension.url
min:
  v: 1
max:
  v: 1
base:
  path:
    v: Extension.url
  min:
    v: 1
  max:
    v: 1
fixed: uri
  v: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.quality