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Resource "fda-vcfeval-comparison" Version "1" (MolecularSequence)

Tags:

XML or JSON representation . provenance for this resource

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

{
  "resourceType" : "MolecularSequence",
  "id" : "fda-vcfeval-comparison",
  "meta" : {
    "versionId" : "1",
    "lastUpdated" : "2018-12-14T02:02:38.582Z"
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: fda-vcfeval-comparison</p><p><b>coordinateSystem</b>: 1</p><p><b>patient</b>: <a>Patient/example</a></p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqId</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NC_000001.11 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000001.11' = 'NC_000001.11)</span></td><td>watson</td><td>10453</td><td>101770080</td></tr></table><h3>Variants</h3><table><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td></tr><tr><td>*</td><td>13116</td><td>13117</td><td>T</td><td>G</td></tr></table><blockquote><p><b>quality</b></p><p><b>type</b>: indel</p><p><b>standardSequence</b>: file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx)</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P)</span></p><p><b>truthTP</b>: 7749</p><p><b>truthFN</b>: 2554</p><p><b>queryFP</b>: 10670</p><p><b>gtFP</b>: 2186</p><p><b>precision</b>: 0.428005</p><p><b>recall</b>: 0.752111</p></blockquote><blockquote><p><b>quality</b></p><p><b>type</b>: snp</p><p><b>standardSequence</b>: file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx)</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P)</span></p><p><b>truthTP</b>: 92106</p><p><b>truthFN</b>: 1247</p><p><b>queryFP</b>: 21744</p><p><b>gtFP</b>: 493</p><p><b>precision</b>: 0.808602</p><p><b>recall</b>: 0.986642</p></blockquote><h3>Repositories</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>Url</b></td><td><b>Name</b></td></tr><tr><td>*</td><td>login</td><td><a>https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y</a></td><td>FDA</td></tr></table></div>"
  },
  "coordinateSystem" : 1,
  "patient" : {
    "reference" : "Patient/example"
  },
  "referenceSeq" : {
    "referenceSeqId" : {
      "coding" : [
        {
          "system" : "http://www.ncbi.nlm.nih.gov/nuccore",
          "code" : "NC_000001.11"
        }
      ]
    },
    "strand" : "watson",
    "windowStart" : 10453,
    "windowEnd" : 101770080
  },
  "variant" : [
    {
      "start" : 13116,
      "end" : 13117,
      "observedAllele" : "T",
      "referenceAllele" : "G"
    }
  ],
  "quality" : [
    {
      "type" : "indel",
      "standardSequence" : {
        "coding" : [
          {
            "system" : "https://precision.fda.gov/files/",
            "code" : "file-BkZxBZ00bpJVk2q6x43b1YBx"
          }
        ]
      },
      "start" : 10453,
      "end" : 101770080,
      "method" : {
        "coding" : [
          {
            "system" : "https://precision.fda.gov/apps/",
            "code" : "app-BxfGF8j02pBZzZxbzZxP725P"
          }
        ],
        "text" : "Vcfeval + Hap.py Comparison"
      },
      "truthTP" : 7749,
      "truthFN" : 2554,
      "queryFP" : 10670,
      "gtFP" : 2186,
      "precision" : 0.428005,
      "recall" : 0.752111
    },
    {
      "type" : "snp",
      "standardSequence" : {
        "coding" : [
          {
            "system" : "https://precision.fda.gov/files/",
            "code" : "file-BkZxBZ00bpJVk2q6x43b1YBx"
          }
        ]
      },
      "start" : 10453,
      "end" : 101770080,
      "method" : {
        "coding" : [
          {
            "system" : "https://precision.fda.gov/apps/",
            "code" : "app-BxfGF8j02pBZzZxbzZxP725P"
          }
        ],
        "text" : "Vcfeval + Hap.py Comparison"
      },
      "truthTP" : 92106,
      "truthFN" : 1247,
      "queryFP" : 21744,
      "gtFP" : 493,
      "precision" : 0.808602,
      "recall" : 0.986642
    }
  ],
  "repository" : [
    {
      "type" : "login",
      "url" : "https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y",
      "name" : "FDA"
    }
  ]
}