Sequence-example-fda-vcfeval.json

MolecularSequence example for vcf and Hap.py comparison on precisionFDA

{
  "resourceType": "MolecularSequence",
  "id": "fda-vcfeval-comparison",
  "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-vcfeval-comparison&quot; </p></div><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><blockquote><p><b>quality</b></p><p><b>type</b>: indel</p><p><b>standardSequence</b>: file-BkZxBZ00bpJVk2q6x43b1YBx <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#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 style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#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 style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#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 style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#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 class=\"grid\"><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 href=\"https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y\">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"
    }
  ]
}