Generated Narrative: StructureDefinition ext-R4B-MolecularSequence.quality Name Flags Card. Type Description & Constraints 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 0..1 Extension True positives from the perspective of the truth data #xD; url 1..1 uri "truthTP" #xD; value[x] 0..1 decimal True positives from the perspective of the truth data #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.quality-definitions.html#Extension.extension:queryTP" title="Slice queryTP: 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.">extension:queryTP 0..1 Extension True positives from the perspective of the query data #xD; url 1..1 uri "queryTP" #xD; value[x] 0..1 decimal True positives from the perspective of the query data #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.quality-definitions.html#Extension.extension:truthFN" title="Slice truthFN: 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.">extension:truthFN 0..1 Extension False negatives #xD; url 1..1 uri "truthFN" #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.quality-definitions.html#Extension.extension:truthFN.value[x]" title="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.">value[x] 0..1 decimal False negatives #xD; extension:queryFP 0..1 Extension False positives #xD; url 1..1 uri "queryFP" #xD; value[x] 0..1 decimal False positives #xD; extension:gtFP 0..1 Extension False positives where the non-REF alleles in the Truth and Query Call Sets match #xD; url 1..1 uri "gtFP" #xD; value[x] 0..1 decimal False positives where the non-REF alleles in the Truth and Query Call Sets match #xD; extension:precision 0..1 Extension Precision of comparison #xD; url 1..1 uri "precision" #xD; value[x] 0..1 decimal Precision of comparison #xD; extension:recall 0..1 Extension Recall of comparison #xD; url 1..1 uri "recall" #xD; value[x] 0..1 decimal Recall of comparison #xD; extension:fScore 0..1 Extension F-score #xD; url 1..1 uri "fScore" #xD; value[x] 0..1 decimal F-score #xD; extension:roc 0..1 Extension Receiver Operator Characteristic (ROC) Curve #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:score 0..* Extension Genotype quality score #xD; url 1..1 uri "score" #xD; value[x] 0..1 integer Genotype quality score #xD; extension:numTP 0..* Extension Roc score true positive numbers #xD; url 1..1 uri "numTP" #xD; value[x] 0..1 integer Roc score true positive numbers #xD; extension:numFP 0..* Extension Roc score false positive numbers #xD; url 1..1 uri "numFP" #xD; value[x] 0..1 integer Roc score false positive numbers #xD; extension:numFN 0..* Extension Roc score false negative numbers #xD; url 1..1 uri "numFN" #xD; value[x] 0..1 integer Roc score false negative numbers #xD; extension:precision 0..* Extension Precision of the GQ score #xD; url 1..1 uri "precision" #xD; value[x] 0..1 decimal Precision of the GQ score #xD; extension:sensitivity 0..* Extension Sensitivity of the GQ score #xD; url 1..1 uri "sensitivity" #xD; value[x] 0..1 decimal Sensitivity of the GQ score #xD; extension:fMeasure 0..* Extension FScore of the GQ score #xD; url 1..1 uri "fMeasure" #xD; value[x] 0..1 decimal FScore of the GQ score #xD; url 1..1 uri "roc" #xD; url 1..1 uri "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.quality" #xD; Documentation for this format
Cross-version Extension for R4B.MolecularSequence.quality for use in FHIR R5
This cross-version extension represents MolecularSequence.quality from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0 for use in FHIR R5.
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)).
`MolecularSequence.quality` has no related element in R5:MolecularSequence
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
Must have either extensions or value[x], not both
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
Additional content defined by implementations
May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and 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.
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.
Source of the definition for the extension code - a logical name or a URL.
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.
Gold standard sequence used for comparing against.
Reference identifier for standard sequence
Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
Which method is used to get sequence quality.
True positives from the perspective of the truth data
True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
True positives from the perspective of the query data
True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.
False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.
False positives where the non-REF alleles in the Truth and Query Call Sets match
The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).
Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
Receiver Operator Characteristic (ROC) Curve
Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
Invidual data point representing the GQ (genotype quality) score threshold.
The number of true positives if the GQ score threshold was set to "score" field value.
The number of false positives if the GQ score threshold was set to "score" field value.
The number of false negatives if the GQ score threshold was set to "score" field value.
Calculated precision if the GQ score threshold was set to "score" field value.
Calculated sensitivity if the GQ score threshold was set to "score" field value.
Calculated fScore if the GQ score threshold was set to "score" field value.
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).