Coord-1base-example.json

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
  },
  "variant": [
    {
      "start": 2,
      "end": 3,
      "observedAllele": "ATG",
      "referenceAllele": "-",
      "cigar": "3I"
    },
    {
      "start": 5,
      "end": 5,
      "observedAllele": "T",
      "referenceAllele": "A",
      "cigar": "3I"
    },
    {
      "start": 7,
      "end": 7,
      "observedAllele": "-",
      "referenceAllele": "T",
      "cigar": "1D"
    }
  ],
  "observedSeq": "ACATGGTAGC"
}