Release 4

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Coord-1base-example.xml

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

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

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Example of a record with 1-based coordinatesystem (id = "coord-1-base")

<?xml version="1.0" encoding="UTF-8"?>

<MolecularSequence xmlns="http://hl7.org/fhir">
    <id value="coord-1-base"/> 
    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative with Details</b> </p> <p> <b> id</b> : coord-1-base</p> <p> <b> type</b> : dna</p> <p> <b> coordinateSystem</b> : 1</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> 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> </text> <type value="dna"/> 
    <coordinateSystem value="1"/> 
    <referenceSeq> 
        <referenceSeqString value="ACGTAGTC"/> 
        <strand value="watson"/> 
        <windowStart value="1"/> 
        <windowEnd value="8"/> 
    </referenceSeq> 
    <variant> 
        <start value="2"/> 
        <end value="3"/> 
        <observedAllele value="ATG"/> 
        <referenceAllele value="-"/> 
        <cigar value="3I"/> 
    </variant> 
    <variant> 
        <start value="5"/> 
        <end value="5"/> 
        <observedAllele value="T"/> 
        <referenceAllele value="A"/> 
        <cigar value="3I"/> 
    </variant> 
    <variant> 
        <start value="7"/> 
        <end value="7"/> 
        <observedAllele value="-"/> 
        <referenceAllele value="T"/> 
        <cigar value="1D"/> 
    </variant>   
    <observedSeq value="ACATGGTAGC"/> 
</MolecularSequence>

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.