Release 4

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU) in it's permanent home (it will always be available at this URL). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3


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=\"\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: coord-0-base</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table><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>0</td><td>8</td></tr></table><blockquote><p><b>variant</b></p><p><b>start</b>: 2</p><p><b>end</b>: 2</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>: 4</p><p><b>end</b>: 5</p><p><b>observedAllele</b>: T</p><p><b>referenceAllele</b>: A</p><p><b>cigar</b>: 1M</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 6</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": 0,
  "referenceSeq": {
    "referenceSeqString": "ACGTAGTC",
    "strand": "watson",
    "windowStart": 0,
    "windowEnd": 8
  "variant": [
      "start": 2,
      "end": 2,
      "observedAllele": "ATG",
      "referenceAllele": "-",
      "cigar": "3I"
      "start": 4,
      "end": 5,
      "observedAllele": "T",
      "referenceAllele": "A",
      "cigar": "1M"
      "start": 6,
      "end": 7,
      "observedAllele": "-",
      "referenceAllele": "T",
      "cigar": "1D"
  "observedSeq": "ACATGGTAGC"

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.