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<StructureDefinition xmlns="http://hl7.org/fhir">
  <id value="719a47ad-6029-46d4-b59e-47dcd2f316c2" />
  <meta>
    <lastUpdated value="2020-02-12T07:25:58.425+00:00" />
  </meta>
  <url value="http://example.org/fhir/StructureDefinition/QcMetrics" />
  <name value="QcMetrics" />
  <status value="draft" />
  <date value="2020-02-12T07:25:55.8166214+00:00" />
  <fhirVersion value="4.0.0" />
  <mapping>
    <identity value="rim" />
    <uri value="http://hl7.org/v3" />
    <name value="RIM Mapping" />
  </mapping>
  <kind value="complex-type" />
  <abstract value="false" />
  <context>
    <type value="element" />
    <expression value="MolecularSequence" />
  </context>
  <type value="Extension" />
  <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Extension" />
  <derivation value="constraint" />
  <differential>
    <element id="Extension.extension">
      <path value="Extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:sequencingType">
      <path value="Extension.extension" />
      <sliceName value="sequencingType" />
      <short value="Sequencing type" />
      <definition value="Sequencing types are three levels of analysis via NGS: whole genome sequencing (WGS), whole exome sequencing (WES), and targeted sequencing. WGS covers all regions of the genome: both coding and noncoding regions. WES covers all coding regions, which is estimated to comprise 1~2% of the genome, yet contains ~85% of recognized disease-related mutations. Targeted sequencing interrogates known disease-associated genes, which is focusing on a limited set of genes to allow greater depth of coverage." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingType.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:sequencingType.extension:sequencingType">
      <path value="Extension.extension.extension" />
      <sliceName value="sequencingType" />
      <short value="Sequencing type" />
      <definition value="Sequencing types are three levels of analysis via NGS: whole genome sequencing (WGS), whole exome sequencing (WES), and targeted sequencing. WGS covers all regions of the genome: both coding and noncoding regions. WES covers all coding regions, which is estimated to comprise 1~2% of the genome, yet contains ~85% of recognized disease-related mutations. Targeted sequencing interrogates known disease-associated genes, which is focusing on a limited set of genes to allow greater depth of coverage." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingType.extension:sequencingType.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="sequencingType" />
    </element>
    <element id="Extension.extension:sequencingType.extension:sequencingType.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sequencingType.extension:targetGene">
      <path value="Extension.extension.extension" />
      <sliceName value="targetGene" />
      <short value="Target gene" />
      <definition value="Sets of genes or gene regions for targeted sequencing. Target gene is represented in accordance with HGNC (HUGO (Human Genome Organization) Gene Nomenclature Committee) and RefSeq (NCBI Reference Sequences)." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingType.extension:targetGene.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="targetGene" />
    </element>
    <element id="Extension.extension:sequencingType.extension:targetGene.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sequencingType.url">
      <path value="Extension.extension.url" />
      <fixedUri value="sequencingType" />
    </element>
    <element id="Extension.extension:sequencingType.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:dnaExtraction">
      <path value="Extension.extension" />
      <sliceName value="dnaExtraction" />
      <short value="DNA extraction method" />
      <definition value="Library preparation is the process of generating DNA fragments to meet the input requirement of sequencing platforms. In general, this workflow involves DNA extraction, DNA quality measurement and library construction. Depending on the purposes of sequencing, library construction methods can vary and sequencing results will be affected. Therefore, for quality control of the data, it is very important to specify the conditions used in each library preparation step." />
      <max value="1" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
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    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaExtractionKit">
      <path value="Extension.extension.extension" />
      <sliceName value="dnaExtractionKit" />
      <short value="DNA extraction kit" />
      <definition value="Product and manufacturer’s name of the DNA extraction kit" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaExtractionKit.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="dnaExtractionKit" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaExtractionKit.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity">
      <path value="Extension.extension.extension" />
      <sliceName value="dnaPurity" />
      <short value="DNA purity" />
      <definition value="The ratio of optical density (OD 260/280, OD 260/230) is used as an indicator of the sample purity" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.extension">
      <path value="Extension.extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.extension:od260280">
      <path value="Extension.extension.extension.extension" />
      <sliceName value="od260280" />
      <short value="OD 260/280" />
      <definition value="The ratio of optical density" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.extension:od260280.url">
      <path value="Extension.extension.extension.extension.url" />
      <fixedUri value="od260280" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.extension:od260280.value[x]">
      <path value="Extension.extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.extension:od260230">
      <path value="Extension.extension.extension.extension" />
      <sliceName value="od260230" />
      <short value="OD 260/230" />
      <definition value="The ratio of optical density" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.extension:od260230.url">
      <path value="Extension.extension.extension.extension.url" />
      <fixedUri value="od260230" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.extension:od260230.value[x]">
      <path value="Extension.extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="dnaPurity" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaPurity.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaIntegrity">
      <path value="Extension.extension.extension" />
      <sliceName value="dnaIntegrity" />
      <short value="DNA integrity" />
      <definition value="The absence of both single or double strand and breaks absence of nucleotide modifications in the DNA, which could be represented by the size and distribution of DNA fragments" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaIntegrity.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="dnaIntegrity" />
    </element>
    <element id="Extension.extension:dnaExtraction.extension:dnaIntegrity.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dnaExtraction.url">
      <path value="Extension.extension.url" />
      <fixedUri value="dnaExtraction" />
    </element>
    <element id="Extension.extension:dnaExtraction.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:libraryConstruction">
      <path value="Extension.extension" />
      <sliceName value="libraryConstruction" />
      <short value="Library construction" />
      <definition value="Library preparation is the process of generating DNA fragments to meet the input requirement of sequencing platforms. In general, this workflow involves DNA extraction, DNA quality measurement and library construction. Depending on the purposes of sequencing, library construction methods can vary and sequencing results will be affected. Therefore, for quality control of the data, it is very important to specify the conditions used in each library preparation step." />
      <max value="1" />
    </element>
    <element id="Extension.extension:libraryConstruction.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryInputAmount">
      <path value="Extension.extension.extension" />
      <sliceName value="libraryInputAmount" />
      <short value="Library input amount" />
      <definition value="Initial input DNA amount for library construction" />
      <max value="1" />
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryInputAmount.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="libraryInputAmount" />
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryInputAmount.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryInsertSize">
      <path value="Extension.extension.extension" />
      <sliceName value="libraryInsertSize" />
      <short value="Library insert size" />
      <definition value="Library insert size used to construct the library, which can be confirmed by QC at the desired size" />
      <max value="1" />
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryInsertSize.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="libraryInsertSize" />
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryInsertSize.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryConstructionKit">
      <path value="Extension.extension.extension" />
      <sliceName value="libraryConstructionKit" />
      <short value="Library construction kit" />
      <definition value="Product and manufacturer’s name of the library construction kit" />
      <max value="1" />
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryConstructionKit.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="libraryConstructionKit" />
    </element>
    <element id="Extension.extension:libraryConstruction.extension:libraryConstructionKit.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:libraryConstruction.url">
      <path value="Extension.extension.url" />
      <fixedUri value="libraryConstruction" />
    </element>
    <element id="Extension.extension:libraryConstruction.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:sequencingInformation">
      <path value="Extension.extension" />
      <sliceName value="sequencingInformation" />
      <short value="Sequencing information" />
      <definition value="Sequencing is the process to run actually NGS platform with pre-processed DNA fragments. Currently available sequencing platforms have different chemistries for sequencing that include sequencing by synthesis (Illumina NGS platforms) and semi-conductor-based sequencing (ThermoFisher’s Ion systems), as well as different detection methods. Despite the similarities in technical performance, differences between platforms exist, notably different DNA input requirements, different cost of reagents, run time, read length, and cost per sample. These differences have implications to the instruments’ capacity to handle low-quality samples, capability of detecting insertions/deletions, and sample throughput. Targeted sequencing technology is used for testing in a part of genomic region, specified with BED format." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
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        <rules value="open" />
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    </element>
    <element id="Extension.extension:sequencingInformation.extension:sequencingInstrument">
      <path value="Extension.extension.extension" />
      <sliceName value="sequencingInstrument" />
      <short value="Sequencing instrument" />
      <definition value="Sequencing device for NGS" />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:sequencingInstrument.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="sequencingInstrument" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:sequencingInstrument.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sequencingInformation.extension:readLength">
      <path value="Extension.extension.extension" />
      <sliceName value="readLength" />
      <short value="Read length" />
      <definition value="Read length in bp" />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:readLength.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="readLength" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:readLength.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:sequencingInformation.extension:sequencingDirection">
      <path value="Extension.extension.extension" />
      <sliceName value="sequencingDirection" />
      <short value="Sequencing direction" />
      <definition value="Single end sequencing (reading in one direction in sequencing) or paired end sequencing (reading in both directions in sequencing)" />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:sequencingDirection.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="sequencingDirection" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:sequencingDirection.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sequencingInformation.extension:runningMode">
      <path value="Extension.extension.extension" />
      <sliceName value="runningMode" />
      <short value="Running mode" />
      <definition value="V4, rapid mode, etc." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:runningMode.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="runningMode" />
    </element>
    <element id="Extension.extension:sequencingInformation.extension:runningMode.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sequencingInformation.url">
      <path value="Extension.extension.url" />
      <fixedUri value="sequencingInformation" />
    </element>
    <element id="Extension.extension:sequencingInformation.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:runningQuality">
      <path value="Extension.extension" />
      <sliceName value="runningQuality" />
      <short value="Running quality information" />
      <definition value="Sequencing is the process to run actually NGS platform with pre-processed DNA fragments. Currently available sequencing platforms have different chemistries for sequencing that include sequencing by synthesis (Illumina NGS platforms) and semi-conductor-based sequencing (ThermoFisher’s Ion systems), as well as different detection methods. Despite the similarities in technical performance, differences between platforms exist, notably different DNA input requirements, different cost of reagents, run time, read length, and cost per sample. These differences have implications to the instruments’ capacity to handle low-quality samples, capability of detecting insertions/deletions, and sample throughput. Targeted sequencing technology is used for testing in a part of genomic region, specified with BED format." />
      <max value="1" />
    </element>
    <element id="Extension.extension:runningQuality.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:runningQuality.extension:errorRate">
      <path value="Extension.extension.extension" />
      <sliceName value="errorRate" />
      <short value="Error rate" />
      <definition value="The rate of spiking in phiX DNA" />
      <max value="1" />
    </element>
    <element id="Extension.extension:runningQuality.extension:errorRate.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="errorRate" />
    </element>
    <element id="Extension.extension:runningQuality.extension:errorRate.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:runningQuality.extension:percentDataQualityQ30">
      <path value="Extension.extension.extension" />
      <sliceName value="percentDataQualityQ30" />
      <short value="Percent data quality &gt;Q30" />
      <definition value="The amount of data expressed as &gt;Q30 in [%]" />
      <max value="1" />
    </element>
    <element id="Extension.extension:runningQuality.extension:percentDataQualityQ30.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="percentDataQualityQ30" />
    </element>
    <element id="Extension.extension:runningQuality.extension:percentDataQualityQ30.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:runningQuality.url">
      <path value="Extension.extension.url" />
      <fixedUri value="runningQuality" />
    </element>
    <element id="Extension.extension:runningQuality.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:dataQuality">
      <path value="Extension.extension" />
      <sliceName value="dataQuality" />
      <short value="Data quality measurement" />
      <definition value="The data processing of NGS is the process to analyze data derived from sequencing platforms and entirely dependent on computing resources. This workflow consists of various processes, such as read alignment, deduplication, variant calling etc. There are many tools available for the purpose of sequencing. Sometimes, in-house tools are generated and used as needed. It is necessary to provide several Bioinformatics QC metrics for the final data to be used for detection of variation." />
      <max value="1" />
    </element>
    <element id="Extension.extension:dataQuality.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:dataQuality.extension:totalReads">
      <path value="Extension.extension.extension" />
      <sliceName value="totalReads" />
      <short value="Total reads" />
      <definition value="The number of sequencing reads in the FASTQ file" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dataQuality.extension:totalReads.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="totalReads" />
    </element>
    <element id="Extension.extension:dataQuality.extension:totalReads.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dataQuality.extension:meanCoverage">
      <path value="Extension.extension.extension" />
      <sliceName value="meanCoverage" />
      <short value="Mean coverage" />
      <definition value="The mean number of sequencing depths aligned at each base of the target area. With hybridization-based capture and whole-genome sequencing, PCR duplicates should be removed from coverage calculations." />
      <max value="1" />
    </element>
    <element id="Extension.extension:dataQuality.extension:meanCoverage.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="meanCoverage" />
    </element>
    <element id="Extension.extension:dataQuality.extension:meanCoverage.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dataQuality.extension:uniformity">
      <path value="Extension.extension.extension" />
      <sliceName value="uniformity" />
      <short value="Uniformity" />
      <definition value="The proportion of base, among the target area, whose number of sequencing read is over x% of the mean coverage and greater than 20x" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dataQuality.extension:uniformity.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="uniformity" />
    </element>
    <element id="Extension.extension:dataQuality.extension:uniformity.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dataQuality.extension:onTargetRate">
      <path value="Extension.extension.extension" />
      <sliceName value="onTargetRate" />
      <short value="On-target rate" />
      <definition value="The proportion of reads being on target from total reads" />
      <max value="1" />
    </element>
    <element id="Extension.extension:dataQuality.extension:onTargetRate.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="onTargetRate" />
    </element>
    <element id="Extension.extension:dataQuality.extension:onTargetRate.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dataQuality.extension:q30">
      <path value="Extension.extension.extension" />
      <sliceName value="q30" />
      <short value="Q30 rate" />
      <definition value="The Q30 rate is the proportion of Phred quality score over 30 for each base in the sequencing read of the alignment file in SAM, BAM, or CRAM format. A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. If Phred assigns a quality score of 30 to a base, the chances that this base is called incorrectly are 1 in 1000." />
      <max value="1" />
    </element>
    <element id="Extension.extension:dataQuality.extension:q30.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="q30" />
    </element>
    <element id="Extension.extension:dataQuality.extension:q30.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:dataQuality.extension:prScore">
      <path value="Extension.extension.extension" />
      <sliceName value="prScore" />
      <short value="PR score" />
      <definition value="Pass rate (PR) score that represents a single unified measure" />
      <comment value="Lee C, Bae JS, Ryu GH, Kim NKD, Park D, Chung J, et al. A Method to Evaluate the Quality of Clinical Gene-Panel Sequencing Data for Single-Nucleotide Variant Detection. J Mol Diagn. 2017;19(5):651-8." />
      <max value="1" />
    </element>
    <element id="Extension.extension:dataQuality.extension:prScore.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="prScore" />
    </element>
    <element id="Extension.extension:dataQuality.url">
      <path value="Extension.extension.url" />
      <fixedUri value="dataQuality" />
    </element>
    <element id="Extension.extension:dataQuality.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:sequencingAlignment">
      <path value="Extension.extension" />
      <sliceName value="sequencingAlignment" />
      <short value="Sequencing alignment" />
      <definition value="The data processing of NGS is the process to analyze data derived from sequencing platforms and entirely dependent on computing resources. This workflow consists of various processes, such as read alignment, deduplication, variant calling etc. There are many tools available for the purpose of sequencing. Sometimes, in-house tools are generated and used as needed. It is necessary to provide several Bioinformatics QC metrics for the final data to be used for detection of variation." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingAlignment.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:sequencingAlignment.extension:mappingAlgorithm">
      <path value="Extension.extension.extension" />
      <sliceName value="mappingAlgorithm" />
      <short value="Mapping algorithm" />
      <definition value="Mapping algorithm used in read mapping step" />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingAlignment.extension:mappingAlgorithm.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="mappingAlgorithm" />
    </element>
    <element id="Extension.extension:sequencingAlignment.extension:mappingAlgorithm.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sequencingAlignment.extension:software">
      <path value="Extension.extension.extension" />
      <sliceName value="software" />
      <short value="Local realignment software and version" />
      <definition value="Software and version used in local realignment" />
      <max value="1" />
    </element>
    <element id="Extension.extension:sequencingAlignment.extension:software.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="software" />
    </element>
    <element id="Extension.extension:sequencingAlignment.extension:software.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sequencingAlignment.url">
      <path value="Extension.extension.url" />
      <fixedUri value="sequencingAlignment" />
    </element>
    <element id="Extension.extension:sequencingAlignment.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:variantCalling">
      <path value="Extension.extension" />
      <sliceName value="variantCalling" />
      <short value="Variant calling" />
      <definition value="The data processing of NGS is the process to analyze data derived from sequencing platforms and entirely dependent on computing resources. This workflow consists of various processes, such as read alignment, deduplication, variant calling etc. There are many tools available for the purpose of sequencing. Sometimes, in-house tools are generated and used as needed. It is necessary to provide several Bioinformatics QC metrics for the final data to be used for detection of variation." />
    </element>
    <element id="Extension.extension:variantCalling.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:variantCalling.extension:software">
      <path value="Extension.extension.extension" />
      <sliceName value="software" />
      <short value="Variant calling software and version" />
      <definition value="Software and version used in variant calling" />
      <max value="1" />
    </element>
    <element id="Extension.extension:variantCalling.extension:software.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="software" />
    </element>
    <element id="Extension.extension:variantCalling.extension:software.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:variantCalling.extension:qualityScore">
      <path value="Extension.extension.extension" />
      <sliceName value="qualityScore" />
      <short value="Variant call quality score" />
      <definition value="Variant call quality score is an estimate of how confident the caller correctly identified that a given genome position displays variation in at least one sample. It is generated during the variant calling step and a requisite component of the VCF." />
      <max value="1" />
    </element>
    <element id="Extension.extension:variantCalling.extension:qualityScore.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="qualityScore" />
    </element>
    <element id="Extension.extension:variantCalling.extension:qualityScore.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:variantCalling.extension:allelicReadPercentage">
      <path value="Extension.extension.extension" />
      <sliceName value="allelicReadPercentage" />
      <short value="Allelic read percentage &amp; ratio" />
      <definition value="Allelic read percentages, including percentage of different variant types (e.g., heterozygous calls, indels, nonsense variants), and portion and ratios of base substitutions" />
      <max value="1" />
    </element>
    <element id="Extension.extension:variantCalling.extension:allelicReadPercentage.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="allelicReadPercentage" />
    </element>
    <element id="Extension.extension:variantCalling.extension:allelicReadPercentage.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="decimal" />
      </type>
    </element>
    <element id="Extension.extension:variantCalling.url">
      <path value="Extension.extension.url" />
      <fixedUri value="variantCalling" />
    </element>
    <element id="Extension.extension:variantCalling.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation">
      <path value="Extension.extension" />
      <sliceName value="variantFilteringAndAnnotation" />
      <short value="Variant filtering and annotation" />
      <definition value="Variant filtering is the process by which variants representing false-positive artifacts of the NGS method are flagged or filtered from the original VCF file on the basis of several sequence alignment and variant calling associated metadata." />
      <max value="1" />
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.extension:germlineFilterCriteria">
      <path value="Extension.extension.extension" />
      <sliceName value="germlineFilterCriteria" />
      <short value="Germline filter criteria" />
      <definition value="Criteria used to distinguish germline mutation from detected mutations" />
      <max value="1" />
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.extension:germlineFilterCriteria.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="germlineFilterCriteria" />
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.extension:germlineFilterCriteria.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.extension:referenceDB">
      <path value="Extension.extension.extension" />
      <sliceName value="referenceDB" />
      <short value="Mutation and annotation database" />
      <definition value="The database is used for identifying clinical relevant mutation, and includes information such as minor allele frequency in the population, predictions of variant effects on protein function or splicing." />
      <max value="1" />
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.extension:referenceDB.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="referenceDB" />
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.extension:referenceDB.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.url">
      <path value="Extension.extension.url" />
      <fixedUri value="variantFilteringAndAnnotation" />
    </element>
    <element id="Extension.extension:variantFilteringAndAnnotation.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.extension:sampleInformation">
      <path value="Extension.extension" />
      <sliceName value="sampleInformation" />
      <max value="1" />
    </element>
    <element id="Extension.extension:sampleInformation.extension">
      <path value="Extension.extension.extension" />
      <slicing>
        <discriminator>
          <type value="value" />
          <path value="url" />
        </discriminator>
        <rules value="open" />
      </slicing>
    </element>
    <element id="Extension.extension:sampleInformation.extension:specimenType">
      <path value="Extension.extension.extension" />
      <sliceName value="specimenType" />
      <short value="Specimen type" />
      <definition value="Type of specimen (e.g. whole blood, cell, urine, fresh cell &amp; tissue) with related data during sample collection (e.g. biopsy, surgical excision, EDTA, heparin), processing (e.g. formalin, centrifugation), and storage (e.g. paraffin block, cryotube)." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sampleInformation.extension:specimenType.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="specimenType" />
    </element>
    <element id="Extension.extension:sampleInformation.extension:samplingDate">
      <path value="Extension.extension.extension" />
      <sliceName value="samplingDate" />
      <short value="Sampling date" />
      <definition value="Sampling date is the date when the specimen was acquired." />
      <max value="1" />
    </element>
    <element id="Extension.extension:sampleInformation.extension:samplingDate.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="samplingDate" />
    </element>
    <element id="Extension.extension:sampleInformation.extension:samplingDate.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="date" />
      </type>
    </element>
    <element id="Extension.extension:sampleInformation.extension:cellline">
      <path value="Extension.extension.extension" />
      <sliceName value="cellline" />
      <short value="Cell Line" />
      <definition value="Cell Line" />
      <max value="1" />
    </element>
    <element id="Extension.extension:sampleInformation.extension:cellline.url">
      <path value="Extension.extension.extension.url" />
      <fixedUri value="cellline" />
    </element>
    <element id="Extension.extension:sampleInformation.extension:cellline.value[x]">
      <path value="Extension.extension.extension.value[x]" />
      <type>
        <code value="string" />
      </type>
    </element>
    <element id="Extension.extension:sampleInformation.url">
      <path value="Extension.extension.url" />
      <fixedUri value="sampleInformation" />
    </element>
    <element id="Extension.extension:sampleInformation.value[x]">
      <path value="Extension.extension.value[x]" />
      <max value="0" />
    </element>
    <element id="Extension.url">
      <path value="Extension.url" />
      <fixedUri value="http://example.org/fhir/StructureDefinition/QcMetrics" />
    </element>
    <element id="Extension.value[x]">
      <path value="Extension.value[x]" />
      <max value="0" />
    </element>
  </differential>
</StructureDefinition>

name : QcMetrics

{

}

<name value="QcMetrics" />