{

"resourceType": "Sequence",
"id": "fda-vcfeval-comparison",
"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>1</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": 1,
  "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"
  }
]

}