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Example MolecularSequence/coord-1-base (JSON)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: Patient

Raw JSON (canonical form + also see JSON Format Specification)

Example of a record with 1-based coordinatesystem

{
  "resourceType": "MolecularSequence",
  "id": "coord-1-base",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"coord-1-base\"> </a></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 MolecularSequence &quot;coord-1-base&quot; </p></div><p><b>type</b>: dna</p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td><td><b>Strand</b></td></tr><tr><td>*</td><td>ACGTAGTC</td><td>1</td><td>8</td><td>watson</td></tr></table><blockquote><p><b>edit</b></p><p><b>start</b>: 2</p><p><b>end</b>: 3</p><p><b>replacementSequence</b>: ATG</p><p><b>replacedSequence</b>: -</p></blockquote><blockquote><p><b>edit</b></p><p><b>start</b>: 5</p><p><b>end</b>: 5</p><p><b>replacementSequence</b>: T</p><p><b>replacedSequence</b>: A</p></blockquote><blockquote><p><b>edit</b></p><p><b>start</b>: 7</p><p><b>end</b>: 7</p><p><b>replacementSequence</b>: -</p><p><b>replacedSequence</b>: T</p></blockquote></blockquote></div>"
  },
  "type": "dna",
  "relative": [
    {
      "coordinateSystem": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA30102-0",
            "display": "1-based character counting"
          }
        ]
      },
      "startingSequence": {
        "sequenceString": "ACGTAGTC",
        "windowStart": 1,
        "windowEnd": 8,
        "strand": "watson"
      },
      "edit": [
        {
          "start": 2,
          "end": 3,
          "replacementSequence": "ATG",
          "replacedSequence": "-"
        },
        {
          "start": 5,
          "end": 5,
          "replacementSequence": "T",
          "replacedSequence": "A"
        },
        {
          "start": 7,
          "end": 7,
          "replacementSequence": "-",
          "replacedSequence": "T"
        }
      ]
    }
  ]
}

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.