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Example MolecularSequence/coord-1-base (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: 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> </text> <type value="dna"/> 
    <relative> 
        <coordinateSystem> 
            <coding> 
                <system value="http://loinc.org"/> 
                <code value="LA30102-0"/> 
                <display value="1-based character counting"/> 
            </coding> 
        </coordinateSystem> 
        <startingSequence> 
            <sequenceString value="ACGTAGTC"/> 
            <windowStart value="1"/> 
            <windowEnd value="8"/> 
            <strand value="watson"/> 
        </startingSequence> 
        <edit> 
            <start value="2"/> 
            <end value="3"/> 
            <replacementSequence value="ATG"/> 
            <replacedSequence value="-"/> 
        </edit> 
        <edit> 
            <start value="5"/> 
            <end value="5"/> 
            <replacementSequence value="T"/> 
            <replacedSequence value="A"/> 
        </edit> 
        <edit> 
            <start value="7"/> 
            <end value="7"/> 
            <replacementSequence value="-"/> 
            <replacedSequence value="T"/> 
        </edit>   
    </relative> 
</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.