Sequence-example-fda-comparisons.xml

Sequence example for vcf comparison on precisionFDA (id = "fda-vcf-comparison")

<Sequence xmlns="http://hl7.org/fhir">
    <id value="fda-vcf-comparison"/>
    <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-vcf-comparison</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>1</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>Score</b></td><td><b>Method</b></td><td><b>TruthTP</b></td><td><b>TruthFN</b></td><td><b>QueryFP</b></td><td><b>GtFP</b></td><td><b>Precision</b></td><td><b>FScore</b></td></tr><tr><td>*</td><td>unknown</td><td>file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bp
              JVk2q6x43b1YBx)</span></td><td>10453</td><td>101770080</td><td>5.000</td><td>VCF Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BqB9XZ8006ZZ2g5KzGXP3fpq' = 'app-BqB9XZ8006ZZ2
              g5KzGXP3fpq)</span></td><td>129481</td><td>3168</td><td>1507</td><td>2186</td><td>0.9885</td><td>0.9823</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></tr><tr><td>*</td><td>login</td><td><a>https://precision.fda.gov/comparisons/1850</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="1"/>
        <windowStart value="10453"/>
        <windowEnd value="101770080"/>
    </referenceSeq>
    <variant>
        <start value="13116"/>
        <end value="13117"/>
        <observedAllele value="T"/>
        <referenceAllele value="G"/>
    </variant>
    <quality>
        <type value="unknown"/>
        <standardSequence>
            <coding>
                <system value="https://precision.fda.gov/files/"/>
                <code value="file-BkZxBZ00bpJVk2q6x43b1YBx"/>
            </coding>
        </standardSequence>
        <start value="10453"/>
        <end value="101770080"/>
        <score>
            <value value="5.000"/>
        </score>
        <method>
            <coding>
                <system value="https://precision.fda.gov/apps/"/>
                <code value="app-BqB9XZ8006ZZ2g5KzGXP3fpq"/>
            </coding>
            <text value="VCF Comparison"/>
        </method>
        <truthTP value="129481"/>
        <truthFN value="3168"/>
        <queryFP value="1507"/>
        <gtFP value="2186"/>
        <precision value="0.9885"/>
        <fScore value="0.9823"/>
    </quality>
    <repository>
        <type value="login"/>
        <url value="https://precision.fda.gov/comparisons/1850"/>
        <name value="FDA"/>
    </repository>
</Sequence>