<PreferredAnalysisRegionsQualityMetrics>
This tag contains several <RegionQualityMetrics> tags for each of the different resolution settings available in NGSengine, core+, exon+ and amplicon.
Inside the <RegionQualityMetrics> the <Noise> tag is available. The <Noise> tag contains several statistics that are also available as part of the quality metrics in the overview screen.
<PreferredAnalysisRegionsQualityMetrics>
<RegionQualityMetrics region="Amplicon" start="-300" end="3203" ampliconFraction="0.8859" analysisCoveredFraction="0.8859" analysisAmpliconFraction="1" qmFraction="0.8859">
<InputData>
<ReadDepth minimum="391" maximum="1193" average="897" median="964" sd="191.883" />
<ReadCoverage forward="1" reverse="1">1</ReadCoverage>
</InputData>
<Noise minimumHeterozygousVsMaxTotalNoise="0.3044”>
<TotalNoiseLevel minimum="0" maximum="0.1163" average="0.0047" median="0.002" sd="0.0118" count="3348" />
<NoiseLevelAtHomozygotes minimum="0" maximum="0.1163" average="0.0047" median="0.002" sd="0.0118" count="3313" />
<NoiseLevelAtHeterozygotes minimum="0" maximum="0.0705" average="0.005" median="0.0014" sd="0.0124" count="35" />
<SecondBaseStatisticsAtHeterozygotes minimum="0.4207" maximum="0.496" average="0.4557" median="0.4512" sd="0.02" count="35" />
</Noise>
<Analysis heterozygousPosnsCount="35" homozygousPosnsCount="3313" ignoredPosnsCount="0">
<Aligning indelsCount="260" isIllumina="True" />
<AnalysisReadDepth minimum="391" maximum="1193" average="897" median="964" sd="191.883" />
<AnalysisReadCoverage forward="1" reverse="1">1</AnalysisReadCoverage>
</Analysis>
</RegionQualityMetrics>
<PreferredAnalysisRegionsQualityMetrics/>
The following statistics are available in the overview when the resolution is set to amplicon:
The Noise corresponds to <TotalNoiseLevel> maximum value.
The Delta Signal to Noise corresponds to <Noise> minimumHeterozygousVsMaxTotalNoise value.
The Estimated Second Allele Percentage corresponds to <SecondBaseStatisticsAtHeterozygots> average value.