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Example MolecularSequence/coord-0-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 0-based coordinatesystem

{
  "resourceType" : "MolecularSequence",
  "id" : "coord-0-base",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"coord-0-base\"> </a><a name=\"hccoord-0-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-0-base&quot; </p></div><p><b>type</b>: dna</p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 0-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30101-2)</span></p><h3>StartingSequences</h3><table class=\"grid\"><tr><td style=\"display: none\">-</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 style=\"display: none\">*</td><td>ACGTAGTC</td><td>0</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>: 2</p><p><b>replacementSequence</b>: ATG</p><p><b>replacedSequence</b>: -</p></blockquote><blockquote><p><b>edit</b></p><p><b>start</b>: 4</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>: 6</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" : "LA30101-2",
        "display" : "0-based character counting"
      }]
    },
    "startingSequence" : {
      "sequenceString" : "ACGTAGTC",
      "windowStart" : 0,
      "windowEnd" : 8,
      "strand" : "watson"
    },
    "edit" : [{
      "start" : 2,
      "end" : 2,
      "replacementSequence" : "ATG",
      "replacedSequence" : "-"
    },
    {
      "start" : 4,
      "end" : 5,
      "replacementSequence" : "T",
      "replacedSequence" : "A"
    },
    {
      "start" : 6,
      "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.