Sequence-example-fda-comparisons.json

MolecularSequence example for vcf comparison on precisionFDA

{
  "resourceType": "MolecularSequence",
  "id": "fda-vcf-comparison",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>id</b>: fda-vcf-comparison</p><p><b>coordinateSystem</b>: 1</p><p><b>patient</b>: <a>Generated Summary: id: example; Medical record number: 12345 (USUAL); active; Peter James Chalmers (OFFICIAL), Jim , Peter James Windsor (MAIDEN); -unknown-(HOME), ph: (03) 5555 6473(WORK), ph: (03) 3410 5613(MOBILE), ph: (03) 5555 8834(OLD); gender: male; birthDate: 1974-12-25; </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><span>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>Score</b></td><td><b>Method</b></td><td><b>TruthTP</b></td><td><b>TruthFN</b></td><td><b>QueryFP</b></td><td><b>GtFP</b></td><td><b>Precision</b></td><td><b>FScore</b></td></tr><tr><td>*</td><td>unknown</td><td><span>file-BkZxBZ00bpJVk2q6x43b1YBx</span></td><td>10453</td><td>101770080</td><td>5.000</td><td><span>VCF Comparison</span></td><td>129481</td><td>3168</td><td>1507</td><td>2186</td><td>0.9885</td><td>0.9823</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></tr><tr><td>*</td><td>login</td><td><a>https://precision.fda.gov/comparisons/1850</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": "unknown",
      "standardSequence": {
        "coding": [
          {
            "system": "https://precision.fda.gov/files/",
            "code": "file-BkZxBZ00bpJVk2q6x43b1YBx"
          }
        ]
      },
      "start": 10453,
      "end": 101770080,
      "score": {
        "value": 5.000
      },
      "method": {
        "coding": [
          {
            "system": "https://precision.fda.gov/apps/",
            "code": "app-BqB9XZ8006ZZ2g5KzGXP3fpq"
          }
        ],
        "text": "VCF Comparison"
      },
      "truthTP": 129481,
      "truthFN": 3168,
      "queryFP": 1507,
      "gtFP": 2186,
      "precision": 0.9885,
      "fScore": 0.9823
    }
  ],
  "repository": [
    {
      "type": "login",
      "url": "https://precision.fda.gov/comparisons/1850",
      "name": "FDA"
    }
  ]
}