Release 4B 5

This page is part of the FHIR Specification (v4.3.0: R4B (v5.0.0: R5 - STU ). The This is the current published version which supercedes in it's permanent home (it will always be available at this version is 5.0.0 . URL). For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R5 R4B R4 R3

Coord-1base-example.json

Example MolecularSequence/coord-1-base (JSON)

Clinical Genomics Work Group Maturity Level : N/A Standards Status : Informative Compartments : 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</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;coord-1-base&quot; </p></div><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>ReferenceSeqString</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>ACGTAGTC</td><td>watson</td><td>1</td><td>8</td></tr></table><blockquote><p><b>variant</b></p><p><b>start</b>: 2</p><p><b>end</b>: 3</p><p><b>observedAllele</b>: ATG</p><p><b>referenceAllele</b>: -</p><p><b>cigar</b>: 3I</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 5</p><p><b>end</b>: 5</p><p><b>observedAllele</b>: T</p><p><b>referenceAllele</b>: A</p><p><b>cigar</b>: 3I</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 7</p><p><b>end</b>: 7</p><p><b>observedAllele</b>: -</p><p><b>referenceAllele</b>: T</p><p><b>cigar</b>: 1D</p></blockquote><p><b>observedSeq</b>: ACATGGTAGC</p></div>"
  },
  "type": "dna",
  "coordinateSystem": 1,
  "referenceSeq": {
    "referenceSeqString": "ACGTAGTC",
    "strand": "watson",
    "windowStart": 1,
    "windowEnd": 8

  "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>"

  },
  "variant": [
    {
      "start": 2,
      "end": 3,
      "observedAllele": "ATG",
      "referenceAllele": "-",
      "cigar": "3I"

  "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,
      "observedAllele": "T",
      "referenceAllele": "A",
      "cigar": "3I"

      "start" : 5,
      "end" : 5,
      "replacementSequence" : "T",
      "replacedSequence" : "A"

    },
    {
      "start": 7,
      "end": 7,
      "observedAllele": "-",
      "referenceAllele": "T",
      "cigar": "1D"
    }
  ],
  "observedSeq": "ACATGGTAGC"

      "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.