Sequence-example-fda-comparisons.xml

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

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