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Sequence-example-fda.xml

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

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MolecularSequence example from precisionFDA (id = "fda-example")

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

<MolecularSequence xmlns="http://hl7.org/fhir">
    <id value="fda-example"/> 
    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative with Details</b> </p> <p> <b> id</b> : fda-example</p> <p> <b> type</b> : dna</p> <p> <b> coordinateSystem</b> : 1</p> <p> <b> patient</b> : <a> Patient/example</a> </p> <h3> ReferenceSeqs</h3> <table> <tr> <td> -</td> <td> <b> ReferenceSeqId</b> </td> <td> <b> Strand</b> </td> <td> <b> WindowStart</b> </td> <td> <b> WindowEnd</b> </td> </tr> <tr> <td> *</td> <td> NC_000001.11 <span> (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000001.11' = 'NC_000001.11)</span> </td> <td> watson</td> <td> 10453</td> <td> 101770080</td> </tr> </table> <h3> Variants</h3> <table> <tr> <td> -</td> <td> <b> Start</b> </td> <td> <b> End</b> </td> <td> <b> ObservedAllele</b> </td> <td> <b> ReferenceAllele</b> </td> </tr> <tr> <td> *</td> <td> 13116</td> <td> 13117</td> <td> T</td> <td> G</td> </tr> </table> <h3> Qualities</h3> <table> <tr> <td> -</td> <td> <b> Type</b> </td> <td> <b> StandardSequence</b> </td> <td> <b> Start</b> </td> <td> <b> End</b> </td> <td> <b> Method</b> </td> <td> <b> TruthTP</b> </td> <td> <b> QueryTP</b> </td> <td> <b> TruthFN</b> </td> <td> <b> QueryFP</b> </td> <td> <b> GtFP</b> </td> <td> <b> Precision</b> </td> <td> <b> Recall</b> </td> <td> <b> FScore</b> </td> </tr> <tr> <td> *</td> <td> snp</td> <td> file-Bk50V4Q0qVb65P0v2VPbfYPZ <span> (Details : {https://precision.fda.gov/files/ code 'file-Bk50V4Q0qVb65P0v2VPbfYPZ' = 'file-Bk50V4Q0qV
              b65P0v2VPbfYPZ)</span> </td> <td> 10453</td> <td> 101770080</td> <td> Vcfeval + Hap.py Comparison <span> (Details : {https://precision.fda.gov/jobs/ code 'job-ByxYPx809jFVy21KJG74Jg3Y' = 'job-ByxYPx809jFVy
              21KJG74Jg3Y)</span> </td> <td> 7749</td> <td> 7984</td> <td> 2554</td> <td> 10670</td> <td> 2186</td> <td> 0.428005</td> <td> 0.752111</td> <td> 0.545551</td> </tr> </table> <h3> Repositories</h3> <table> <tr> <td> -</td> <td> <b> Type</b> </td> <td> <b> Url</b> </td> <td> <b> Name</b> </td> <td> <b> VariantsetId</b> </td> </tr> <tr> <td> *</td> <td> login</td> <td> <a> https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38</a> </td> <td> FDA</td> <td> file-Bx37ZK009P4bX5g3qjkFZV38</td> </tr> </table> </div> </text> <type value="dna"/> 
    <coordinateSystem value="1"/> 
    <patient> 
        <reference value="Patient/example"/> 
    </patient> 
    <referenceSeq> 
        <referenceSeqId> 
          <coding> 
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> 
            <code value="NC_000001.11"/> 
          </coding> 
        </referenceSeqId> 
        <strand value="watson"/> 
        <windowStart value="10453"/> 
        <windowEnd value="101770080"/> 
    </referenceSeq> 
    <variant> 
        <start value="13116"/> 
        <end value="13117"/> 
        <observedAllele value="T"/> 
        <referenceAllele value="G"/> 
    </variant> 
    <quality> 
        <type value="snp"/> 
        <standardSequence> 
            <coding> 
                <system value="https://precision.fda.gov/files/"/> 
                <code value="file-Bk50V4Q0qVb65P0v2VPbfYPZ"/> 
            </coding> 
        </standardSequence> 
        <start value="10453"/> 
        <end value="101770080"/> 
        <method> 
            <coding> 
                <system value="https://precision.fda.gov/jobs/"/> 
                <code value="job-ByxYPx809jFVy21KJG74Jg3Y"/> 
            </coding> 
            <text value="Vcfeval + Hap.py Comparison"/> 
        </method> 
        <truthTP value="7749"/> 
        <queryTP value="7984"/> 
        <truthFN value="2554"/> 
        <queryFP value="10670"/> 
        <gtFP value="2186"/> 
        <precision value="0.428005"/> 
        <recall value="0.752111"/> 
        <fScore value="0.545551"/> 
    </quality> 
    <repository> 
        <type value="login"/> 
        <url value="https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38"/> 
        <name value="FDA"/> 
        <variantsetId value="file-Bx37ZK009P4bX5g3qjkFZV38"/> 
    </repository> 
</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.