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Resource "fda-example" Version "1" (MolecularSequence)

Tags:

XML or JSON representation . provenance for this resource

Generated Narrative with Details

id: fda-example

type: dna

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

Qualities

-TypeStandardSequenceStartEndMethodTruthTPQueryTPTruthFNQueryFPGtFPPrecisionRecallFScore
*snpfile-Bk50V4Q0qVb65P0v2VPbfYPZ (Details : {https://precision.fda.gov/files/ code 'file-Bk50V4Q0qVb65P0v2VPbfYPZ' = 'file-Bk50V4Q0qVb65P0v2VPbfYPZ)10453101770080Vcfeval + Hap.py Comparison (Details : {https://precision.fda.gov/jobs/ code 'job-ByxYPx809jFVy21KJG74Jg3Y' = 'job-ByxYPx809jFVy21KJG74Jg3Y)7749798425541067021860.4280050.7521110.545551

Repositories

-TypeUrlNameVariantsetId
*loginhttps://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38FDAfile-Bx37ZK009P4bX5g3qjkFZV38

{
  "resourceType" : "MolecularSequence",
  "id" : "fda-example",
  "meta" : {
    "versionId" : "1",
    "lastUpdated" : "2018-12-14T02:02:38.520Z"
  },
  "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-example</p><p><b>type</b>: dna</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><h3>Qualities</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>StandardSequence</b></td><td><b>Start</b></td><td><b>End</b></td><td><b>Method</b></td><td><b>TruthTP</b></td><td><b>QueryTP</b></td><td><b>TruthFN</b></td><td><b>QueryFP</b></td><td><b>GtFP</b></td><td><b>Precision</b></td><td><b>Recall</b></td><td><b>FScore</b></td></tr><tr><td>*</td><td>snp</td><td>file-Bk50V4Q0qVb65P0v2VPbfYPZ <span>(Details : {https://precision.fda.gov/files/ code 'file-Bk50V4Q0qVb65P0v2VPbfYPZ' = 'file-Bk50V4Q0qVb65P0v2VPbfYPZ)</span></td><td>10453</td><td>101770080</td><td>Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/jobs/ code 'job-ByxYPx809jFVy21KJG74Jg3Y' = 'job-ByxYPx809jFVy21KJG74Jg3Y)</span></td><td>7749</td><td>7984</td><td>2554</td><td>10670</td><td>2186</td><td>0.428005</td><td>0.752111</td><td>0.545551</td></tr></table><h3>Repositories</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>Url</b></td><td><b>Name</b></td><td><b>VariantsetId</b></td></tr><tr><td>*</td><td>login</td><td><a>https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38</a></td><td>FDA</td><td>file-Bx37ZK009P4bX5g3qjkFZV38</td></tr></table></div>"
  },
  "type" : "dna",
  "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" : "snp",
      "standardSequence" : {
        "coding" : [
          {
            "system" : "https://precision.fda.gov/files/",
            "code" : "file-Bk50V4Q0qVb65P0v2VPbfYPZ"
          }
        ]
      },
      "start" : 10453,
      "end" : 101770080,
      "method" : {
        "coding" : [
          {
            "system" : "https://precision.fda.gov/jobs/",
            "code" : "job-ByxYPx809jFVy21KJG74Jg3Y"
          }
        ],
        "text" : "Vcfeval + Hap.py Comparison"
      },
      "truthTP" : 7749,
      "queryTP" : 7984,
      "truthFN" : 2554,
      "queryFP" : 10670,
      "gtFP" : 2186,
      "precision" : 0.428005,
      "recall" : 0.752111,
      "fScore" : 0.545551
    }
  ],
  "repository" : [
    {
      "type" : "login",
      "url" : "https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38",
      "name" : "FDA",
      "variantsetId" : "file-Bx37ZK009P4bX5g3qjkFZV38"
    }
  ]
}