Sequence-example-fda-vcfeval.xml

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

<Sequence 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 with Details</b></p><p><b>id</b>: fda-vcfeval-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><blockquote><p><b>quality</b></p><p><b>type</b>: indel</p><p><b>standardSequence</b>: file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bp
            JVk2q6x43b1YBx)</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZz
            ZxbzZxP725P)</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>: file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bp
            JVk2q6x43b1YBx)</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZz
            ZxbzZxP725P)</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="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="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>
</Sequence>