<?xml version="1.0"?>
<AnalysisJobInfo xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Version="0">
  <AlignmentFolder>D:\Illumina\MiSeqAnalysis\200319_M02006_0024_000000000-J397M\Data\Intensities\BaseCalls\Alignment</AlignmentFolder>
  <CompletionTime>2020-03-20T14:12:56.0676129+01:00</CompletionTime>
  <RTARunInfo Version="2">
    <Run Id="200319_M02006_0024_000000000-J397M" Number="24">
      <Flowcell>000000000-J397M</Flowcell>
      <Instrument>M02006</Instrument>
      <Date>200319</Date>
      <Reads>
        <Read NumCycles="151" StartFromCycle="1" EndWithCycle="151" IsIndexedRead="N" />
        <Read NumCycles="8" StartFromCycle="1" EndWithCycle="8" IsIndexedRead="Y" />
        <Read NumCycles="8" StartFromCycle="1" EndWithCycle="8" IsIndexedRead="Y" />
        <Read NumCycles="151" StartFromCycle="1" EndWithCycle="151" IsIndexedRead="N" />
      </Reads>
      <FlowcellLayout LaneCount="1" SurfaceCount="2" SwathCount="1" TileCount="14" />
      <AlignToPhiX />
    </Run>
  </RTARunInfo>
  <RunFolder>D:\Illumina\MiSeqAnalysis\200319_M02006_0024_000000000-J397M</RunFolder>
  <Sheet>
    <Type>MiSeq</Type>
    <WorkflowType>GenerateFASTQ</WorkflowType>
    <Header>
      <Chemistry>Amplicon</Chemistry>
      <Date>19.03.2020</Date>
    </Header>
  </Sheet>
  <StartTime>2020-03-20T14:10:17.9473915+01:00</StartTime>
  <Workflow>
    <WorkflowSettings>
      <AdapterSequences />
      <AdapterSequences2 />
      <TrimFastq>false</TrimFastq>
      <FastQInput>false</FastQInput>
      <StitchReads>false</StitchReads>
      <MaximumThreadCount>0</MaximumThreadCount>
      <ReadTrimQualityScoreLevel>0</ReadTrimQualityScoreLevel>
      <ReverseComplement>false</ReverseComplement>
      <VarCallerSettings>
        <Filters>
          <FilterOutSingleProbePoolVariants>false</FilterOutSingleProbePoolVariants>
          <FilterOutSingleStrandVariants>false</FilterOutSingleStrandVariants>
          <IndelRepeatFilterCutoff>8</IndelRepeatFilterCutoff>
          <MinQScore>0</MinQScore>
          <MinimumCoverageDepthEmitCutoff>-1</MinimumCoverageDepthEmitCutoff>
          <MinimumDepthCutoff>-1</MinimumDepthCutoff>
          <MinimumGQCutoff>0</MinimumGQCutoff>
          <MinimumGQXCutoff>0</MinimumGQXCutoff>
          <MinimumMQCutoff>-1</MinimumMQCutoff>
          <MinimumQDCutoff>0</MinimumQDCutoff>
          <MinimumQualCutoff>-1</MinimumQualCutoff>
          <MinimumQualityEmitCutoff>-1</MinimumQualityEmitCutoff>
          <OnlyCallInROI>false</OnlyCallInROI>
          <OnlyUseProperPairs>false</OnlyUseProperPairs>
          <CallPhasedSNVs>false</CallPhasedSNVs>
          <StrandBiasFilterCutoff>0</StrandBiasFilterCutoff>
          <MaxSizePhasedSNV>100</MaxSizePhasedSNV>
          <QualityModel>Poisson</QualityModel>
          <VariantFrequencyEmitCutoff>0.1</VariantFrequencyEmitCutoff>
          <VariantFrequencyFilterCutoff>0.2</VariantFrequencyFilterCutoff>
          <FilterOffTargetVariants>false</FilterOffTargetVariants>
        </Filters>
        <Annotation>MARS</Annotation>
        <SVAnnotation>None</SVAnnotation>
        <AnnotationSource>refseq</AnnotationSource>
        <AnnotateHGMD>false</AnnotateHGMD>
        <OutputGenomeVcf>false</OutputGenomeVcf>
        <GVcfBlockCompression>true</GVcfBlockCompression>
      </VarCallerSettings>
      <VariantCaller>None</VariantCaller>
      <ComputePerTileStats>true</ComputePerTileStats>
      <CompressBam>false</CompressBam>
    </WorkflowSettings>
    <Analysis>GenerateFASTQ</Analysis>
    <WorkflowVersion>0.0.0.0</WorkflowVersion>
  </Workflow>
  <Warning>Warning: %Q30 is low (17.4%); secondary analysis results may be adversely affected.  Please review the primary analysis results in SAV to troubleshoot the run</Warning>
  <AnalysisSoftwareVersion>2.6.2.3</AnalysisSoftwareVersion>
  <RTAOutputFolder>D:\Illumina\MiSeqOutput\200319_M02006_0024_000000000-J397M</RTAOutputFolder>
</AnalysisJobInfo>