Sequence-example-fda.json

MolecularSequence example from precisionFDA

{
  "resourceType": "MolecularSequence",
  "id": "fda-example",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource &quot;fda-example&quot; </p></div><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</p><p><b>patient</b>: <a href=\"patient-example.html\">Patient/example</a> &quot;Peter CHALMERS&quot;</p><h3>ReferenceSeqs</h3><table class=\"grid\"><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 style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NC_000001.11)</span></td><td>watson</td><td>10453</td><td>101770080</td></tr></table><h3>Variants</h3><table class=\"grid\"><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 class=\"grid\"><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 style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#file-Bk50V4Q0qVb65P0v2VPbfYPZ)</span></td><td>10453</td><td>101770080</td><td>Vcfeval + Hap.py Comparison <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#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 class=\"grid\"><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 href=\"https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38\">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"
    }
  ]
}