Sequence-example-fda-vcfeval.xml

MolecularSequence example for vcf and Hap.py comparison on precisionFDA (id = "fda-vcfeval-comparison")

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

<MolecularSequence xmlns="http://hl7.org/fhir">
    <id value="fda-vcfeval-comparison"/> 
    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative</b> </p> <p> <b> coordinateSystem</b> : 1</p> <p> <b> patient</b> : <a> Generated Summary: Medical record number: 12345 (USUAL); active; Peter James Chalmers
           (OFFICIAL), Jim , Peter James Windsor (MAIDEN); , Phone: (03) 5555 6473, Phone: (03) 3410
           5613, Phone: (03) 5555 8834; gender: male; birthDate: 1974-12-25; </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> <span> 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> <blockquote> <p> <b> quality</b> </p> <p> <b> type</b> : indel</p> <p> <b> standardSequence</b> : <span> file-BkZxBZ00bpJVk2q6x43b1YBx</span> </p> <p> <b> start</b> : 10453</p> <p> <b> end</b> : 101770080</p> <p> <b> method</b> : <span> Vcfeval + Hap.py Comparison</span> </p> <p> <b> truthTP</b> : 7749</p> <p> <b> truthFN</b> : 2554</p> <p> <b> queryFP</b> : 10670</p> <p> <b> gtFP</b> : 2186</p> <p> <b> precision</b> : 0.428005</p> <p> <b> recall</b> : 0.752111</p> </blockquote> <blockquote> <p> <b> quality</b> </p> <p> <b> type</b> : snp</p> <p> <b> standardSequence</b> : <span> file-BkZxBZ00bpJVk2q6x43b1YBx</span> </p> <p> <b> start</b> : 10453</p> <p> <b> end</b> : 101770080</p> <p> <b> method</b> : <span> Vcfeval + Hap.py Comparison</span> </p> <p> <b> truthTP</b> : 92106</p> <p> <b> truthFN</b> : 1247</p> <p> <b> queryFP</b> : 21744</p> <p> <b> gtFP</b> : 493</p> <p> <b> precision</b> : 0.808602</p> <p> <b> recall</b> : 0.986642</p> </blockquote> <h3> Repositories</h3> <table> <tr> <td> -</td> <td> <b> Type</b> </td> <td> <b> Url</b> </td> <td> <b> Name</b> </td> </tr> <tr> <td> *</td> <td> login</td> <td> <a> https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y</a> </td> <td> FDA</td> </tr> </table> </div> </text> <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="indel"/> 
        <standardSequence> 
            <coding> 
                <system value="https://precision.fda.gov/files/"/> 
                <code value="file-BkZxBZ00bpJVk2q6x43b1YBx"/> 
            </coding> 
        </standardSequence> 
        <start value="10453"/> 
        <end value="101770080"/> 
        <method> 
            <coding> 
                <system value="https://precision.fda.gov/apps/"/> 
                <code value="app-BxfGF8j02pBZzZxbzZxP725P"/> 
            </coding> 
            <text value="Vcfeval + Hap.py Comparison"/> 
        </method> 
        <truthTP value="7749"/> 
        <truthFN value="2554"/> 
        <queryFP value="10670"/> 
        <gtFP value="2186"/> 
        <precision value="0.428005"/> 
        <recall value="0.752111"/> 
    </quality> 
    <quality> 
        <type value="snp"/> 
        <standardSequence> 
            <coding> 
                <system value="https://precision.fda.gov/files/"/> 
                <code value="file-BkZxBZ00bpJVk2q6x43b1YBx"/> 
            </coding> 
        </standardSequence> 
        <start value="10453"/> 
        <end value="101770080"/> 
        <method> 
            <coding> 
                <system value="https://precision.fda.gov/apps/"/> 
                <code value="app-BxfGF8j02pBZzZxbzZxP725P"/> 
            </coding> 
            <text value="Vcfeval + Hap.py Comparison"/> 
        </method> 
        <truthTP value="92106"/> 
        <truthFN value="1247"/> 
        <queryFP value="21744"/> 
        <gtFP value="493"/> 
        <precision value="0.808602"/> 
        <recall value="0.986642"/> 
    </quality> 
    <repository> 
        <type value="login"/> 
        <url value="https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y"/> 
        <name value="FDA"/> 
    </repository> 
</MolecularSequence>