<?xml version="1.0" encoding="UTF-8"?>
<AnalysisMethodContainer xmlns="www.AppliedBiosystems.com"><appVersion>3.6</appVersion><fileVersion>1.0</fileVersion><xmlAnalysisMethod><analysisMethodName>CFEU2_3130 Analysis Method</analysisMethodName><createdDate>1217245952000</createdDate><modifiedDate>1217245952000</modifiedDate><userName>gm</userName><applicationMode>3</applicationMode><signalProcessMode>2</signalProcessMode><analysisFullRange>false</analysisFullRange><analysisStartPt>1600</analysisStartPt><analysisStopPt>8000</analysisStopPt><sizeCallAllSizes>true</sizeCallAllSizes><sizeCallStartSize>0.0</sizeCallStartSize><sizeCallStopSize>1000.0</sizeCallStopSize><smoothValue>8</smoothValue><thresholdMap><Key>Sample Genotype Quality</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Sample Genotype Quality</name><result>Pass</result></QualityThreshold></thresholdMap><thresholdMap><Key>Homozygous Mutation</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Homozygous Mutation</name><result>Pass</result></QualityThreshold></thresholdMap><thresholdMap><Key>Sample File Not Found</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Sample File Not Found</name><result>Pass</result></QualityThreshold></thresholdMap><thresholdMap><Key>Sizing Quality</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Sizing Quality</name><result>Pass</result></QualityThreshold></thresholdMap><thresholdMap><Key>Size Standard Not Found</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Size Standard Not Found</name><result>Pass</result></QualityThreshold></thresholdMap><thresholdMap><Key>Off-scale</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Off-scale</name><result>Pass</result></QualityThreshold></thresholdMap><thresholdMap><Key>Matrix Not Found</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Matrix Not Found</name><result>Pass</result></QualityThreshold></thresholdMap><thresholdMap><Key>Genotype Quality</Key><QualityThreshold><goodIndicator>0.75</goodIndicator><badIndicator>0.25</badIndicator><name>Genotype Quality</name><result>Pass</result></QualityThreshold></thresholdMap><multiComponenterParameter><AnalysisParameter/></multiComponenterParameter><baselinerParameter><AnalysisParameter/><windowSize>51</windowSize><spikeSize>5</spikeSize></baselinerParameter><peakDetectorParameter><AnalysisParameter/><degree>3</degree><window>15</window><degreeTetri>3</degreeTetri><windowTetri>9</windowTetri><minHeightBlue>100</minHeightBlue><minHeightGreen>50</minHeightGreen><minHeightYellow>100</minHeightYellow><minHeightRed>50</minHeightRed><minHeightOrange>5</minHeightOrange><minWidth>2</minWidth><tauB>0.0</tauB><tauE>0.0</tauE><heightAutoDetermined>true</heightAutoDetermined></peakDetectorParameter><sizeMatcherParameter><AnalysisParameter/></sizeMatcherParameter><sizeCallerParameter><AnalysisParameter/><sizeCallMethod>Local Southern</sizeCallMethod></sizeCallerParameter><alleleCallerParameter><AnalysisParameter/><notStrMarker_cutOffValue>0.25</notStrMarker_cutOffValue><notStrMarker_cutOffValue_b>0.25</notStrMarker_cutOffValue_b><notStrMarker_cutOffValue_g>0.25</notStrMarker_cutOffValue_g><notStrMarker_cutOffValue_y>0.25</notStrMarker_cutOffValue_y><notStrMarker_cutOffValue_r>0.25</notStrMarker_cutOffValue_r><notStrMarker_cutOffValue_o>0.25</notStrMarker_cutOffValue_o><notStrMarker_plusADistance>0.0</notStrMarker_plusADistance><notStrMarker_plusADistanceRight>0.0</notStrMarker_plusADistanceRight><notStrMarker_plusARatio>0.0</notStrMarker_plusARatio><notStrMarker_minusADistance>0.0</notStrMarker_minusADistance><notStrMarker_minusADistanceRight>0.0</notStrMarker_minusADistanceRight><notStrMarker_minusARatio>0.0</notStrMarker_minusARatio><notStrMarker_stutterDistance>3.0</notStrMarker_stutterDistance><notStrMarker_stutterDistanceRight>0.0</notStrMarker_stutterDistanceRight><notStrMarker_stutterRatio>0.0</notStrMarker_stutterRatio><diNucleotide_cutOffValue>0.32</diNucleotide_cutOffValue><diNucleotide_plusADistance>1.6</diNucleotide_plusADistance><diNucleotide_plusADistanceRight>0.0</diNucleotide_plusADistanceRight><diNucleotide_plusARatio>0.95</diNucleotide_plusARatio><diNucleotide_minusADistance>0.0</diNucleotide_minusADistance><diNucleotide_minusADistanceRight>0.0</diNucleotide_minusADistanceRight><diNucleotide_minusARatio>0.0</diNucleotide_minusARatio><diNucleotide_stutterDistance>3.0</diNucleotide_stutterDistance><diNucleotide_stutterDistanceRight>0.0</diNucleotide_stutterDistanceRight><diNucleotide_stutterRatio>0.95</diNucleotide_stutterRatio><triNucleotide_cutOffValue>0.2</triNucleotide_cutOffValue><triNucleotide_plusADistance>1.6</triNucleotide_plusADistance><triNucleotide_plusADistanceRight>0.0</triNucleotide_plusADistanceRight><triNucleotide_plusARatio>0.95</triNucleotide_plusARatio><triNucleotide_minusADistance>0.0</triNucleotide_minusADistance><triNucleotide_minusADistanceRight>0.0</triNucleotide_minusADistanceRight><triNucleotide_minusARatio>0.0</triNucleotide_minusARatio><triNucleotide_stutterDistance>3.5</triNucleotide_stutterDistance><triNucleotide_stutterDistanceRight>0.0</triNucleotide_stutterDistanceRight><triNucleotide_stutterRatio>0.95</triNucleotide_stutterRatio><tetriNucleotide_cutOffValue>0.25</tetriNucleotide_cutOffValue><tetriNucleotide_plusADistance>1.6</tetriNucleotide_plusADistance><tetriNucleotide_plusADistanceRight>0.0</tetriNucleotide_plusADistanceRight><tetriNucleotide_plusARatio>0.95</tetriNucleotide_plusARatio><tetriNucleotide_minusADistance>1.6</tetriNucleotide_minusADistance><tetriNucleotide_minusADistanceRight>0.0</tetriNucleotide_minusADistanceRight><tetriNucleotide_minusARatio>0.95</tetriNucleotide_minusARatio><tetriNucleotide_stutterDistance>4.5</tetriNucleotide_stutterDistance><tetriNucleotide_stutterDistanceRight>0.0</tetriNucleotide_stutterDistanceRight><tetriNucleotide_stutterRatio>0.15</tetriNucleotide_stutterRatio><useMarkerStutterPercentage>false</useMarkerStutterPercentage><binSet>CFEU2</binSet><warningPeakHeightRatioThreshold>0.5</warningPeakHeightRatioThreshold><warningPeakHeightThresholdHomozygous>200.0</warningPeakHeightThresholdHomozygous><warningPeakHeightThresholdHeterozygous>100.0</warningPeakHeightThresholdHeterozygous><warningMaxAlleleNumber>2</warningMaxAlleleNumber><warningPeakWidthThreshold>1.5</warningPeakWidthThreshold><warningDoublePeakThreshold>0.5</warningDoublePeakThreshold><warningBleedthroughHeightThreshold>0.1</warningBleedthroughHeightThreshold><warningBleedthroughScanThreshold>1</warningBleedthroughScanThreshold><warningCrossTalkHeightThreshold>0.05</warningCrossTalkHeightThreshold><warningCrossTalkScanThreshold>1</warningCrossTalkScanThreshold><warningMinPeakWidthThreshold>0.3</warningMinPeakWidthThreshold><snapShotSNPCutOffValue>0.3</snapShotSNPCutOffValue><olaCutOffValue>0.3</olaCutOffValue><olaRemovePlusLabel>false</olaRemovePlusLabel><olaPlusFrom>0.0</olaPlusFrom><olaPlusTo>1.6</olaPlusTo><olaPlusPercentage>5.0</olaPlusPercentage><olaRemoveMinusLabel>false</olaRemoveMinusLabel><olaMinusFrom>0.0</olaMinusFrom><olaMinusTo>3.0</olaMinusTo><olaMinusPercent>5.0</olaMinusPercent><zipChuteLadderCutoffValue>0.3</zipChuteLadderCutoffValue><zipchuteCutOffValue>0.3</zipchuteCutOffValue><needClustering>true</needClustering><withinRunClustering>false</withinRunClustering><clusterCVThreshold>0.95</clusterCVThreshold><clusterSigmaSeparation>6.0</clusterSigmaSeparation><clusterHardyWeinbergP>0.01</clusterHardyWeinbergP><clusterNumberCluster>2.0</clusterNumberCluster><clusterAngleDifference>1.2</clusterAngleDifference><clusterCallRate>0.8</clusterCallRate><clusterSignalMedian>2.4</clusterSignalMedian><clusterModelFit>0.8</clusterModelFit><clusterSampleSignalThreshold>500.0</clusterSampleSignalThreshold><clusterSampleTemplateThreshold>0.01</clusterSampleTemplateThreshold><clearRangeBlueDyeFrom>0.0</clearRangeBlueDyeFrom><clearRangeBlueDyeTo>0.0</clearRangeBlueDyeTo><clearRangeGreenDyeFrom>0.0</clearRangeGreenDyeFrom><clearRangeGreenDyeTo>0.0</clearRangeGreenDyeTo><clearRangeYellowDyeFrom>0.0</clearRangeYellowDyeFrom><clearRangeYellowDyeTo>0.0</clearRangeYellowDyeTo><clearRangeRedDyeFrom>0.0</clearRangeRedDyeFrom><clearRangeRedDyeTo>0.0</clearRangeRedDyeTo><clearRangeOrangeDyeFrom>0.0</clearRangeOrangeDyeFrom><clearRangeOrangeDyeTo>0.0</clearRangeOrangeDyeTo><pentaNucleotide_cutOffValue>0.25</pentaNucleotide_cutOffValue><pentaNucleotide_plusADistance>1.6</pentaNucleotide_plusADistance><pentaNucleotide_plusADistanceRight>0.0</pentaNucleotide_plusADistanceRight><pentaNucleotide_plusARatio>0.95</pentaNucleotide_plusARatio><pentaNucleotide_minusADistance>1.6</pentaNucleotide_minusADistance><pentaNucleotide_minusADistanceRight>0.0</pentaNucleotide_minusADistanceRight><pentaNucleotide_minusARatio>0.95</pentaNucleotide_minusARatio><pentaNucleotide_stutterDistance>5.5</pentaNucleotide_stutterDistance><pentaNucleotide_stutterDistanceRight>0.0</pentaNucleotide_stutterDistanceRight><pentaNucleotide_stutterRatio>0.15</pentaNucleotide_stutterRatio><hexNucleotide_cutOffValue>0.25</hexNucleotide_cutOffValue><hexNucleotide_plusADistance>1.6</hexNucleotide_plusADistance><hexNucleotide_plusADistanceRight>0.0</hexNucleotide_plusADistanceRight><hexNucleotide_plusARatio>0.95</hexNucleotide_plusARatio><hexNucleotide_minusADistance>1.6</hexNucleotide_minusADistance><hexNucleotide_minusADistanceRight>0.0</hexNucleotide_minusADistanceRight><hexNucleotide_minusARatio>0.95</hexNucleotide_minusARatio><hexNucleotide_stutterDistance>6.5</hexNucleotide_stutterDistance><hexNucleotide_stutterDistanceRight>0.0</hexNucleotide_stutterDistanceRight><hexNucleotide_stutterRatio>0.15</hexNucleotide_stutterRatio><binWidth>1.0</binWidth><aflpAlleleLabelling>true</aflpAlleleLabelling><aflpThreshold>100.0</aflpThreshold><aflpThresholdType>1</aflpThresholdType><aflpKeepLargeVariantCommonAllele>false</aflpKeepLargeVariantCommonAllele><aflpVariantRatio>1.8</aflpVariantRatio><aflpGeneratingPanelsSample>1</aflpGeneratingPanelsSample><subsettingSampleColumn>2</subsettingSampleColumn><subsettingSampleOperation>1</subsettingSampleOperation><aflpThresholdOne>0.0</aflpThresholdOne><aflpThresholdTwo>0.0</aflpThresholdTwo><aflpThresholdThree>0.0</aflpThresholdThree><aflpThresholdFour>0.0</aflpThresholdFour><aflpThresholdFive>0.0</aflpThresholdFive><aflpThresholdSix>0.0</aflpThresholdSix><aflpThresholdSeven>0.0</aflpThresholdSeven><aflpThresholdEight>0.0</aflpThresholdEight><aflpLabel>0</aflpLabel><aflpLabelOne>1</aflpLabelOne><aflpRangeStart>50.0</aflpRangeStart><aflpRangeEnd>500.0</aflpRangeEnd><aflpKeepCommonAllele>false</aflpKeepCommonAllele><aflpGeneratingPanels>false</aflpGeneratingPanels><signalNormalizationMethod>0</signalNormalizationMethod><signalNormalizationScope>2</signalNormalizationScope><blueDyeSelected>false</blueDyeSelected><greenDyeSelected>false</greenDyeSelected><yellowDyeSelected>false</yellowDyeSelected><redDyeSelected>false</redDyeSelected><orangeDyeSelected>false</orangeDyeSelected><useMLCV>false</useMLCV></alleleCallerParameter><qualityValueProcessParameter><AnalysisParameter/><bleedThroughQualityWeight>0.5</bleedThroughQualityWeight><splitPeakQualityWeight>0.5</splitPeakQualityWeight><spikyPeakQualityWeight>0.5</spikyPeakQualityWeight><oneBPQualityWeight>0.5</oneBPQualityWeight><broadPeakQualityWeight>0.5</broadPeakQualityWeight><backgroundPeakQualityWeight>0.5</backgroundPeakQualityWeight><binningQualityWeight>0.8</binningQualityWeight><peakAbsoluteHeightQualityWeight>0.5</peakAbsoluteHeightQualityWeight><peakHeightRatioQualityWeight>0.5</peakHeightRatioQualityWeight><offscaleQualityWeight>0.5</offscaleQualityWeight><doublePeakQualityWeight>0.5</doublePeakQualityWeight><narrowBinQualityWeight>0.5</narrowBinQualityWeight><controlAlleleQualityWeight>0.5</controlAlleleQualityWeight><overlapQualityWeight>0.5</overlapQualityWeight><crossTalkPeakQualityWeight>0.5</crossTalkPeakQualityWeight></qualityValueProcessParameter><geneScanAnalyzerParameter><AnalysisParameter/><analysisParams_fullRange>true</analysisParams_fullRange><analysisParams_analStartPt>0</analysisParams_analStartPt><analysisParams_analStopPt>10000</analysisParams_analStopPt><analysisParams_allSizes>true</analysisParams_allSizes><analysisParams_startSize>0</analysisParams_startSize><analysisParams_stopSize>1000</analysisParams_stopSize><analysisParams_multicomponent>true</analysisParams_multicomponent><analysisParams_baseline>true</analysisParams_baseline><analysisParams_smoothValue>0</analysisParams_smoothValue><analysisParams_pkThreshold_blue>50</analysisParams_pkThreshold_blue><analysisParams_pkThreshold_green>50</analysisParams_pkThreshold_green><analysisParams_pkThreshold_yellow>50</analysisParams_pkThreshold_yellow><analysisParams_pkThreshold_red>50</analysisParams_pkThreshold_red><analysisParams_pkThreshold_orange>50</analysisParams_pkThreshold_orange><analysisParams_pkMinPeakWidth>3</analysisParams_pkMinPeakWidth><analysisParams_sizeCallMethod>4</analysisParams_sizeCallMethod><analysisParams_pkCorrMethod>0</analysisParams_pkCorrMethod><analysisParams_pkCorrLimit>30</analysisParams_pkCorrLimit></geneScanAnalyzerParameter></xmlAnalysisMethod></AnalysisMethodContainer>