R4 Ballot #2 (Mixed Normative/Trial use)

This page is part of the FHIR Specification (v3.5.0: R4 Ballot #2). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R4B R4 R3

Sequence-example-fda-vcfeval

Clinical Genomics Work GroupMaturity Level: N/ABallot Status: InformativeCompartments: Not linked to any defined compartments

This is the narrative for the resource. See also the XML, JSON or Turtle format. This example conforms to the profile Sequence.

Generated Narrative with Details

id: fda-vcfeval-comparison

coordinateSystem: 1

patient: Patient/example

ReferenceSeqs

-ReferenceSeqIdStrandWindowStartWindowEnd
*NC_000001.11 (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000001.11' = 'NC_000001.11)watson10453101770080

Variants

-StartEndObservedAlleleReferenceAllele
*1311613117TG

quality

type: indel

standardSequence: file-BkZxBZ00bpJVk2q6x43b1YBx (Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx)

start: 10453

end: 101770080

method: Vcfeval + Hap.py Comparison (Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P)

truthTP: 7749

truthFN: 2554

queryFP: 10670

gtFP: 2186

precision: 0.428005

recall: 0.752111

quality

type: snp

standardSequence: file-BkZxBZ00bpJVk2q6x43b1YBx (Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx)

start: 10453

end: 101770080

method: Vcfeval + Hap.py Comparison (Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P)

truthTP: 92106

truthFN: 1247

queryFP: 21744

gtFP: 493

precision: 0.808602

recall: 0.986642

Repositories

-TypeUrlName
*loginhttps://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3YFDA

 

 

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.