Coord-1base-example.xml

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

<Sequence 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>1</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="1"/>
        <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"/>
</Sequence>