diff --git a/build.xml b/build.xml index 8e9de2272..9a66d4699 100644 --- a/build.xml +++ b/build.xml @@ -955,8 +955,8 @@ - - + + diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index aaf7d1e6e..039ca565a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -26,7 +26,9 @@ package org.broadinstitute.sting.gatk; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.samtools.*; +import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.*; @@ -35,8 +37,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.datasources.reads.*; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.samples.SampleDB; import org.broadinstitute.sting.gatk.executive.MicroScheduler; import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.filters.ReadFilter; @@ -45,6 +45,8 @@ import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; +import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; +import org.broadinstitute.sting.gatk.samples.SampleDB; import org.broadinstitute.sting.gatk.samples.SampleDBBuilder; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; @@ -190,7 +192,7 @@ public class GenomeAnalysisEngine { private BaseRecalibration baseRecalibration = null; public BaseRecalibration getBaseRecalibration() { return baseRecalibration; } public boolean hasBaseRecalibration() { return baseRecalibration != null; } - public void setBaseRecalibration(File recalFile) { baseRecalibration = new BaseRecalibration(recalFile); } + public void setBaseRecalibration(File recalFile, int quantizationLevels) { baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels); } /** * Actually run the GATK with the specified walker. @@ -216,7 +218,7 @@ public class GenomeAnalysisEngine { // if the use specified an input BQSR recalibration table then enable on the fly recalibration if (this.getArguments().BQSR_RECAL_FILE != null) - setBaseRecalibration(this.getArguments().BQSR_RECAL_FILE); + setBaseRecalibration(this.getArguments().BQSR_RECAL_FILE, this.getArguments().quantizationLevels); // Determine how the threads should be divided between CPU vs. IO. determineThreadAllocation(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 670f04bda..3a1408d59 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -193,6 +193,16 @@ public class GATKArgumentCollection { @Input(fullName="BQSR", shortName="BQSR", required=false, doc="Filename for the input covariates table recalibration .csv file which enables on the fly base quality score recalibration") public File BQSR_RECAL_FILE = null; // BUGBUG: need a better argument name once we decide how BQSRs v1 and v2 will live in the code base simultaneously + /** + * Turns on the base quantization module. It requires a recalibration report (-BQSR). + * + * A value of 0 here means "do not quantize". + * Any value greater than zero will be used to recalculate the quantization using this many levels. + * Negative values do nothing (i.e. quantize using the recalibration report's quantization level -- same as not providing this parameter at all) + */ + @Argument(fullName="quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels.", required=false) + public int quantizationLevels = -1; + @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false) public byte defaultBaseQualities = -1; diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java index 376064cdb..1290319e2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java @@ -191,6 +191,16 @@ public class ReferenceContext { return basesCache; } + /** + * All the bases in the window from the current base forward to the end of the window. + */ + public byte[] getForwardBases() { + final byte[] bases = getBases(); + final int mid = locus.getStart() - window.getStart(); + // todo -- warning of performance problem, especially if this is called over and over + return new String(bases).substring(mid).getBytes(); + } + @Deprecated public char getBaseAsChar() { return (char)getBase(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java index 393230ee4..afe847583 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java @@ -19,13 +19,19 @@ import java.util.Map; public class QuantizationInfo { private List quantizedQuals; private List empiricalQualCounts; + int quantizationLevels; - public QuantizationInfo(List quantizedQuals, List empiricalQualCounts) { + public QuantizationInfo(List quantizedQuals, List empiricalQualCounts, int quantizationLevels) { this.quantizedQuals = quantizedQuals; this.empiricalQualCounts = empiricalQualCounts; + this.quantizationLevels = quantizationLevels; + } + + public QuantizationInfo(List quantizedQuals, List empiricalQualCounts) { + this(quantizedQuals, empiricalQualCounts, calculateQuantizationLevels(quantizedQuals)); } - public QuantizationInfo(Map> keysAndTablesMap, int nLevels) { + public QuantizationInfo(Map> keysAndTablesMap, int quantizationLevels) { final Long [] qualHistogram = new Long[QualityUtils.MAX_QUAL_SCORE+1]; // create a histogram with the empirical quality distribution for (int i = 0; i < qualHistogram.length; i++) qualHistogram[i] = 0L; @@ -46,7 +52,9 @@ public class QuantizationInfo { qualHistogram[empiricalQual] += nObservations; // add the number of observations for every key } empiricalQualCounts = Arrays.asList(qualHistogram); // histogram with the number of observations of the empirical qualities - quantizeQualityScores(nLevels); + quantizeQualityScores(quantizationLevels); + + this.quantizationLevels = quantizationLevels; } @@ -55,10 +63,20 @@ public class QuantizationInfo { quantizedQuals = quantizer.getOriginalToQuantizedMap(); // map with the original to quantized qual map (using the standard number of levels in the RAC) } + public void noQuantization() { + this.quantizationLevels = QualityUtils.MAX_QUAL_SCORE; + for (int i = 0; i < this.quantizationLevels; i++) + quantizedQuals.set(i, (byte) i); + } + public List getQuantizedQuals() { return quantizedQuals; } + public int getQuantizationLevels() { + return quantizationLevels; + } + public GATKReportTable generateReportTable() { GATKReportTable quantizedTable = new GATKReportTable(RecalDataManager.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map"); quantizedTable.addPrimaryKey(RecalDataManager.QUALITY_SCORE_COLUMN_NAME); @@ -71,4 +89,16 @@ public class QuantizationInfo { } return quantizedTable; } + + private static int calculateQuantizationLevels(List quantizedQuals) { + byte lastByte = -1; + int quantizationLevels = 0; + for (byte q : quantizedQuals) { + if (q != lastByte) { + quantizationLevels++; + lastByte = q; + } + } + return quantizationLevels; + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java index 8a5213cb7..0b66bb182 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java @@ -25,8 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; * OTHER DEALINGS IN THE SOFTWARE. */ -import org.broadinstitute.sting.utils.QualityUtils; - /** * Created by IntelliJ IDEA. * User: rpoplin @@ -37,10 +35,10 @@ import org.broadinstitute.sting.utils.QualityUtils; public class RecalDatum extends RecalDatumOptimized { - private double estimatedQReported; // estimated reported quality score based on combined data's individual q-reporteds and number of observations - private double empiricalQuality; // the empirical quality for datums that have been collapsed together (by read group and reported quality, for example) + private double estimatedQReported; // estimated reported quality score based on combined data's individual q-reporteds and number of observations + private double empiricalQuality; // the empirical quality for datums that have been collapsed together (by read group and reported quality, for example) - private static final int SMOOTHING_CONSTANT = 1; // used when calculating empirical qualities to avoid division by zero + private static final int SMOOTHING_CONSTANT = 1; // used when calculating empirical qualities to avoid division by zero //--------------------------------------------------------------------------------------------------------------- // @@ -110,7 +108,11 @@ public class RecalDatum extends RecalDatumOptimized { } private double calcExpectedErrors() { - return (double) this.numObservations * QualityUtils.qualToProb(estimatedQReported); + return (double) this.numObservations * qualToErrorProb(estimatedQReported); + } + + private double qualToErrorProb(final double qual) { + return Math.pow(10.0, qual / -10.0); } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java index b0e0087b0..c434cc96b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java @@ -139,7 +139,7 @@ public class RecalibrationReport { columnNamesOrderedList.add(RecalDataManager.COVARIATE_VALUE_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.COVARIATE_NAME_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.EVENT_TYPE_COLUMN_NAME); - return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList); + return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList, false); } /** @@ -154,7 +154,7 @@ public class RecalibrationReport { columnNamesOrderedList.add(RecalDataManager.READGROUP_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.QUALITY_SCORE_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.EVENT_TYPE_COLUMN_NAME); - return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList); + return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList, false); } /** @@ -168,7 +168,7 @@ public class RecalibrationReport { ArrayList columnNamesOrderedList = new ArrayList(2); columnNamesOrderedList.add(RecalDataManager.READGROUP_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.EVENT_TYPE_COLUMN_NAME); - return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList); + return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList, true); } /** @@ -179,7 +179,7 @@ public class RecalibrationReport { * @param columnNamesOrderedList a list of columns to read from the report table and build as key for this particular table * @return a lookup table indexed by bitsets containing the empirical quality and estimated quality reported for every key. */ - private Map genericRecalTableParsing(BQSRKeyManager keyManager, GATKReportTable reportTable, ArrayList columnNamesOrderedList) { + private Map genericRecalTableParsing(BQSRKeyManager keyManager, GATKReportTable reportTable, ArrayList columnNamesOrderedList, boolean hasEstimatedQReportedColumn) { Map result = new HashMap(reportTable.getNumRows()*2); for (Object primaryKey : reportTable.getPrimaryKeys()) { @@ -192,10 +192,13 @@ public class RecalibrationReport { long nObservations = (Long) reportTable.get(primaryKey, RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME); long nErrors = (Long) reportTable.get(primaryKey, RecalDataManager.NUMBER_ERRORS_COLUMN_NAME); - double estimatedQReported = (Double) reportTable.get(primaryKey, RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME); double empiricalQuality = (Double) reportTable.get(primaryKey, RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME); - RecalDatum recalDatum = new RecalDatum(nObservations, nErrors, estimatedQReported, empiricalQuality); + double estimatedQReported = hasEstimatedQReportedColumn ? // the estimatedQreported column only exists in the ReadGroup table + (Double) reportTable.get(primaryKey, RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table + Byte.parseByte((String) reportTable.get(primaryKey, RecalDataManager.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table + + RecalDatum recalDatum = new RecalDatum(nObservations, nErrors, estimatedQReported, empiricalQuality); result.put(bitKey, recalDatum); } return result; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java index 0867d949e..c93e780bf 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java @@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.utils.MathUtils; -import java.util.ArrayList; import java.util.Arrays; /** @@ -42,12 +41,13 @@ public class AlleleFrequencyCalculationResult { // These variables are intended to contain the MLE and MAP (and their corresponding allele counts) of the site over all alternate alleles private double log10MLE; private double log10MAP; - final private int[] alleleCountsOfMLE; - final private int[] alleleCountsOfMAP; + private final int[] alleleCountsOfMLE; + private final int[] alleleCountsOfMAP; // The posteriors seen, not including that of AF=0 - // TODO -- better implementation needed here (see below) - private ArrayList log10PosteriorMatrixValues = new ArrayList(100000); + private static final int POSTERIORS_CACHE_SIZE = 5000; + private final double[] log10PosteriorMatrixValues = new double[POSTERIORS_CACHE_SIZE]; + private int currentPosteriorsCacheIndex = 0; private Double log10PosteriorMatrixSum = null; // These variables are intended to contain the likelihood/posterior probability for the site's being monomorphic (i.e. AF=0 for all alternate alleles) @@ -69,14 +69,9 @@ public class AlleleFrequencyCalculationResult { return log10MAP; } - public double getLog10PosteriorMatrixSum() { + public double getLog10PosteriorsMatrixSumWithoutAFzero() { if ( log10PosteriorMatrixSum == null ) { - // TODO -- we absolutely need a better implementation here as we don't want to store all values from the matrix in memory; - // TODO -- will discuss with the team what the best option is - final double[] tmp = new double[log10PosteriorMatrixValues.size()]; - for ( int i = 0; i < tmp.length; i++ ) - tmp[i] = log10PosteriorMatrixValues.get(i); - log10PosteriorMatrixSum = MathUtils.log10sumLog10(tmp); + log10PosteriorMatrixSum = MathUtils.log10sumLog10(log10PosteriorMatrixValues, 0, currentPosteriorsCacheIndex); } return log10PosteriorMatrixSum; } @@ -103,7 +98,7 @@ public class AlleleFrequencyCalculationResult { alleleCountsOfMLE[i] = 0; alleleCountsOfMAP[i] = 0; } - log10PosteriorMatrixValues.clear(); + currentPosteriorsCacheIndex = 0; log10PosteriorMatrixSum = null; } @@ -116,7 +111,8 @@ public class AlleleFrequencyCalculationResult { } public void updateMAPifNeeded(final double log10LofK, final int[] alleleCountsForK) { - log10PosteriorMatrixValues.add(log10LofK); + addToPosteriorsCache(log10LofK); + if ( log10LofK > log10MAP ) { log10MAP = log10LofK; for ( int i = 0; i < alleleCountsForK.length; i++ ) @@ -124,6 +120,18 @@ public class AlleleFrequencyCalculationResult { } } + private void addToPosteriorsCache(final double log10LofK) { + // add to the cache + log10PosteriorMatrixValues[currentPosteriorsCacheIndex++] = log10LofK; + + // if we've filled up the cache, then condense by summing up all of the values and placing the sum back into the first cell + if ( currentPosteriorsCacheIndex == POSTERIORS_CACHE_SIZE ) { + final double temporarySum = MathUtils.log10sumLog10(log10PosteriorMatrixValues, 0, currentPosteriorsCacheIndex); + log10PosteriorMatrixValues[0] = temporarySum; + currentPosteriorsCacheIndex = 1; + } + } + public void setLog10LikelihoodOfAFzero(final double log10LikelihoodOfAFzero) { this.log10LikelihoodOfAFzero = log10LikelihoodOfAFzero; if ( log10LikelihoodOfAFzero > log10MLE ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java index 5f374e597..5d6cf9f7d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java @@ -72,6 +72,8 @@ import static java.lang.Math.pow; */ public class DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering implements Cloneable { + public final static double DEFAULT_PCR_ERROR_RATE = 1e-4; + protected final static int FIXED_PLOIDY = 2; protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1; protected final static double ploidyAdjustment = log10(FIXED_PLOIDY); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 58b8af493..9f606cdfb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -45,7 +45,7 @@ public class UnifiedArgumentCollection { * het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2 */ @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false) - public Double heterozygosity = DiploidSNPGenotypePriors.HUMAN_HETEROZYGOSITY; + public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY; /** * The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily @@ -53,7 +53,7 @@ public class UnifiedArgumentCollection { * effectively acts as a cap on the base qualities. */ @Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false) - public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE; + public Double PCR_error = DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.DEFAULT_PCR_ERROR_RATE; /** * Specifies how to determine the alternate allele to use for genotyping diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index e561fc511..f26dfe22e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -51,6 +51,9 @@ import java.util.*; public class UnifiedGenotyperEngine { public static final String LOW_QUAL_FILTER_NAME = "LowQual"; + public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3; + public static final double HUMAN_INDEL_HETEROZYGOSITY = 1e-4; + public enum OUTPUT_MODE { /** produces calls only at variant sites */ EMIT_VARIANTS_ONLY, @@ -324,7 +327,7 @@ public class UnifiedGenotyperEngine { } else { phredScaledConfidence = QualityUtils.phredScaleErrorRate(PofF); if ( Double.isInfinite(phredScaledConfidence) ) { - final double sum = AFresult.getLog10PosteriorMatrixSum(); + final double sum = AFresult.getLog10PosteriorsMatrixSumWithoutAFzero(); phredScaledConfidence = (MathUtils.compareDoubles(sum, 0.0) == 0 ? 0 : -10.0 * sum); } } @@ -367,7 +370,7 @@ public class UnifiedGenotyperEngine { // the overall lod //double overallLog10PofNull = AFresult.log10AlleleFrequencyPosteriors[0]; - double overallLog10PofF = AFresult.getLog10PosteriorMatrixSum(); + double overallLog10PofF = AFresult.getLog10PosteriorsMatrixSumWithoutAFzero(); //if ( DEBUG_SLOD ) System.out.println("overallLog10PofF=" + overallLog10PofF); List alternateAllelesToUse = builder.make().getAlternateAlleles(); @@ -378,7 +381,7 @@ public class UnifiedGenotyperEngine { afcm.get().getLog10PNonRef(vcForward, getAlleleFrequencyPriors(model), AFresult); //double[] normalizedLog10Posteriors = MathUtils.normalizeFromLog10(AFresult.log10AlleleFrequencyPosteriors, true); double forwardLog10PofNull = AFresult.getLog10PosteriorOfAFzero(); - double forwardLog10PofF = AFresult.getLog10PosteriorMatrixSum(); + double forwardLog10PofF = AFresult.getLog10PosteriorsMatrixSumWithoutAFzero(); //if ( DEBUG_SLOD ) System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF); // the reverse lod @@ -387,7 +390,7 @@ public class UnifiedGenotyperEngine { afcm.get().getLog10PNonRef(vcReverse, getAlleleFrequencyPriors(model), AFresult); //normalizedLog10Posteriors = MathUtils.normalizeFromLog10(AFresult.log10AlleleFrequencyPosteriors, true); double reverseLog10PofNull = AFresult.getLog10PosteriorOfAFzero(); - double reverseLog10PofF = AFresult.getLog10PosteriorMatrixSum(); + double reverseLog10PofF = AFresult.getLog10PosteriorsMatrixSumWithoutAFzero(); //if ( DEBUG_SLOD ) System.out.println("reverseLog10PofNull=" + reverseLog10PofNull + ", reverseLog10PofF=" + reverseLog10PofF); double forwardLod = forwardLog10PofF + reverseLog10PofNull - overallLog10PofF; @@ -422,7 +425,7 @@ public class UnifiedGenotyperEngine { public static double[] generateNormalizedPosteriors(final AlleleFrequencyCalculationResult AFresult, final double[] normalizedPosteriors) { normalizedPosteriors[0] = AFresult.getLog10PosteriorOfAFzero(); - normalizedPosteriors[1] = AFresult.getLog10PosteriorMatrixSum(); + normalizedPosteriors[1] = AFresult.getLog10PosteriorsMatrixSumWithoutAFzero(); return MathUtils.normalizeFromLog10(normalizedPosteriors); } @@ -620,8 +623,6 @@ public class UnifiedGenotyperEngine { } - public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3; - public static final double HUMAN_INDEL_HETEROZYGOSITY = 1e-4; protected double getTheta( final GenotypeLikelihoodsCalculationModel.Model model ) { if( model.name().contains("SNP") ) return HUMAN_SNP_HETEROZYGOSITY; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index b0877d893..6c7922ea5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -116,6 +116,15 @@ public class VariantEvalWalker extends RodWalker implements Tr @ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); + /** + * Some analyses want to count overlap not with dbSNP (which is in general very open) but + * actually want to itemize their overlap specifically with a set of gold standard sites + * such as HapMap, OMNI, or the gold standard indels. Theis argument provides a mechanism + * for communicating which file to use + */ + @Input(fullName="goldStandard", shortName = "gold", doc="Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison", required=false) + public RodBinding goldStandard = null; + // Help arguments @Argument(fullName="list", shortName="ls", doc="List the available eval modules and exit", required=false) protected Boolean LIST = false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java index 49b865c31..786b7296b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java @@ -56,6 +56,12 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { @DataPoint(description = "Number of singleton Indels", format = "%d") public int n_singleton_indels = 0; + @DataPoint(description = "Number of Indels overlapping gold standard sites", format = "%d") + public int n_indels_matching_gold_standard = 0; + + @DataPoint(description = "Percent of indels overlapping gold standard sites") + public String gold_standard_matching_rate; + // counts 1 for each site where the number of alleles > 2 public int nMultiIndelSites = 0; @@ -71,18 +77,6 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { @DataPoint(description = "Indel novelty rate") public String indel_novelty_rate; - @DataPoint(description = "1 to 2 bp indel ratio") - public String ratio_of_1_to_2_bp_indels; - - @DataPoint(description = "1 to 3 bp indel ratio") - public String ratio_of_1_to_3_bp_indels; - - @DataPoint(description = "2 to 3 bp indel ratio") - public String ratio_of_2_to_3_bp_indels; - - @DataPoint(description = "1 and 2 to 3 bp indel ratio") - public String ratio_of_1_and_2_to_3_bp_indels; - @DataPoint(description = "Frameshift percent") public String frameshift_rate_for_coding_indels; @@ -92,9 +86,6 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { @DataPoint(description = "Insertion to deletion ratio") public String insertion_to_deletion_ratio; - @DataPoint(description = "Insertion to deletion ratio for 1 bp events") - public String insertion_to_deletion_ratio_for_1bp_indels; - // // Frameshifts // @@ -116,9 +107,25 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { int nSNPHets = 0, nSNPHoms = 0, nIndelHets = 0, nIndelHoms = 0; int nKnownIndels = 0, nInsertions = 0; - int n1bpInsertions = 0, n1bpDeletions = 0; - int[] countByLength = new int[]{0, 0, 0, 0}; // note that the first element isn't used + int[] insertionCountByLength = new int[]{0, 0, 0, 0}; // note that the first element isn't used + int[] deletionCountByLength = new int[]{0, 0, 0, 0}; // note that the first element isn't used + + // - Since 1 & 2 bp insertions and 1 & 2 bp deletions are equally likely to cause a + // downstream frameshift, if we make the simplifying assumptions that 3 bp ins + // and 3bp del (adding/subtracting 1 AA in general) are roughly comparably + // selected against, we should see a consistent 1+2 : 3 bp ratio for insertions + // as for deletions, and certainly would expect consistency between in/dels that + // multiple methods find and in/dels that are unique to one method (since deletions + // are more common and the artifacts differ, it is probably worth looking at the totals, + // overlaps and ratios for insertions and deletions separately in the methods + // comparison and in this case don't even need to make the simplifying in = del functional assumption + + @DataPoint(description = "ratio of 1 and 2 bp insertions to 3 bp insertions") + public String ratio_of_1_and_2_to_3_bp_insertions; + + @DataPoint(description = "ratio of 1 and 2 bp deletions to 3 bp deletions") + public String ratio_of_1_and_2_to_3_bp_deletions; public final static int LARGE_INDEL_SIZE_THRESHOLD = 10; @@ -150,11 +157,11 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { } break; case INDEL: + final VariantContext gold = getWalker().goldStandard == null ? null : tracker.getFirstValue(getWalker().goldStandard); if ( eval.isComplexIndel() ) break; // don't count complex substitutions nIndelSites++; if ( ! eval.isBiallelic() ) nMultiIndelSites++; - if ( variantWasSingleton(eval) ) n_singleton_indels++; // collect information about het / hom ratio for ( final Genotype g : eval.getGenotypes() ) { @@ -164,15 +171,14 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { for ( Allele alt : eval.getAlternateAlleles() ) { n_indels++; // +1 for each alt allele - + if ( variantWasSingleton(eval) ) n_singleton_indels++; if ( comp != null ) nKnownIndels++; // TODO -- make this test allele specific? + if ( gold != null ) n_indels_matching_gold_standard++; // ins : del ratios final int alleleSize = alt.length() - eval.getReference().length(); if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference()); if ( alleleSize > 0 ) nInsertions++; - if ( alleleSize == 1 ) n1bpInsertions++; - if ( alleleSize == -1 ) n1bpDeletions++; // requires snpEFF annotations if ( eval.getAttributeAsString("SNPEFF_GENE_BIOTYPE", "missing").equals("protein_coding") ) { @@ -193,6 +199,7 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { n_large_deletions++; // update the baby histogram + final int[] countByLength = alleleSize < 0 ? deletionCountByLength : insertionCountByLength; final int absSize = Math.abs(alleleSize); if ( absSize < countByLength.length ) countByLength[absSize]++; @@ -210,18 +217,18 @@ public class IndelSummary extends VariantEvaluator implements StandardEval { percent_of_sites_with_more_than_2_alleles = Utils.formattedRatio(nMultiIndelSites, nIndelSites); SNP_to_indel_ratio = Utils.formattedRatio(n_SNPs, n_indels); SNP_to_indel_ratio_for_singletons = Utils.formattedRatio(n_singleton_SNPs, n_singleton_indels); + + gold_standard_matching_rate = Utils.formattedNoveltyRate(n_indels_matching_gold_standard, n_indels); indel_novelty_rate = Utils.formattedNoveltyRate(nKnownIndels, n_indels); - ratio_of_1_to_2_bp_indels = Utils.formattedRatio(countByLength[1], countByLength[2]); - ratio_of_1_to_3_bp_indels = Utils.formattedRatio(countByLength[1], countByLength[3]); - ratio_of_2_to_3_bp_indels = Utils.formattedRatio(countByLength[2], countByLength[3]); - ratio_of_1_and_2_to_3_bp_indels = Utils.formattedRatio(countByLength[1] + countByLength[2], countByLength[3]); frameshift_rate_for_coding_indels = Utils.formattedPercent(n_coding_indels_frameshifting, n_coding_indels_in_frame + n_coding_indels_frameshifting); + ratio_of_1_and_2_to_3_bp_deletions = Utils.formattedRatio(deletionCountByLength[1] + deletionCountByLength[2], deletionCountByLength[3]); + ratio_of_1_and_2_to_3_bp_insertions = Utils.formattedRatio(insertionCountByLength[1] + insertionCountByLength[2], insertionCountByLength[3]); + SNP_het_to_hom_ratio = Utils.formattedRatio(nSNPHets, nSNPHoms); indel_het_to_hom_ratio = Utils.formattedRatio(nIndelHets, nIndelHoms); insertion_to_deletion_ratio = Utils.formattedRatio(nInsertions, n_indels - nInsertions); - insertion_to_deletion_ratio_for_1bp_indels = Utils.formattedRatio(n1bpInsertions, n1bpDeletions); insertion_to_deletion_ratio_for_large_indels = Utils.formattedRatio(n_large_insertions, n_large_deletions); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java new file mode 100644 index 000000000..fe4f7641f --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java @@ -0,0 +1,59 @@ +/* + * Copyright (c) 2012, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +/** + * Stratifies the eval RODs into sites where the indel is 1 bp in length and those where the event is 2+. + * all non indel events go into all bins, so that SNP counts can be used as contrasts in eval modules. + */ +public class OneBPIndel extends VariantStratifier { + private final static List ALL = Arrays.asList((Object)"all", (Object)"one.bp", (Object)"two.plus.bp"); + private final static List ONE_BP = Arrays.asList((Object)"all", (Object)"one.bp"); + private final static List TWO_PLUS_BP = Arrays.asList((Object)"all", (Object)"two.plus.bp"); + + @Override + public void initialize() { + states.addAll(ALL); + } + + @Override + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (eval != null && eval.isIndel()) { + for ( int l : eval.getIndelLengths() ) + if ( l > 1 ) + return TWO_PLUS_BP; // someone is too long + return ONE_BP; // all lengths are one + } else + return ALL; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java new file mode 100644 index 000000000..834c02b83 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java @@ -0,0 +1,67 @@ +/* + * Copyright (c) 2012, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; + +import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; + +import java.util.Arrays; +import java.util.List; + +/** + * Stratifies the eval RODs into sites that are tandem repeats + */ +public class TandemRepeat extends VariantStratifier { + private final static List JUST_ALL = Arrays.asList((Object)"all"); + private final static List ALL = Arrays.asList((Object)"all", (Object)"is.repeat", (Object)"not.repeat"); + private final static List REPEAT = Arrays.asList((Object)"all", (Object)"is.repeat"); + private final static List NOT_REPEAT = Arrays.asList((Object)"all", (Object)"not.repeat"); + + @Override + public void initialize() { + states.addAll(ALL); + } + + @Override + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if ( eval == null || ! eval.isIndel() ) + return ALL; + else if ( VariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) { + print("REPEAT", eval, ref); + return REPEAT; + } else { + print("NOT A REPEAT", eval, ref); + return NOT_REPEAT; + } + } + + private final void print(String prefix, VariantContext eval, ReferenceContext ref) { +// String alleles = ParsingUtils.sortList(eval.getAlleles()).toString(); +// this.getVariantEvalWalker().getLogger().info(prefix + ": " + "pos=" + eval.getStart() + " alleles=" + alleles + " ref=" + new String(ref.getForwardBases())); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index a8c622a96..03c7d279b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -27,12 +27,11 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; @@ -41,6 +40,7 @@ public class Haplotype { protected final double[] quals; private GenomeLoc genomeLocation = null; private HashMap readLikelihoodsPerSample = null; + private HashMap eventMap = null; private boolean isRef = false; private Cigar cigar; private int alignmentStartHapwrtRef; @@ -97,6 +97,14 @@ public class Haplotype { return readLikelihoodsPerSample.keySet(); } + public HashMap getEventMap() { + return eventMap; + } + + public void setEventMap( final HashMap eventMap ) { + this.eventMap = eventMap; + } + public boolean isReference() { return isRef; } diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java index 74f147127..c6ca39f4b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java @@ -224,10 +224,6 @@ public class IndelUtils { return inds; } - public static String[] getIndelClassificationNames() { - return COLUMN_KEYS; - } - public static String getIndelClassificationName(int k) { if (k >=0 && k < COLUMN_KEYS.length) return COLUMN_KEYS[k]; @@ -235,35 +231,6 @@ public class IndelUtils { throw new ReviewedStingException("Invalid index when trying to get indel classification name"); } - public static boolean isATExpansion(VariantContext vc, ReferenceContext ref) { - ArrayList inds = findEventClassificationIndex(vc, ref); - - boolean isIt = false; - for (int k : inds) { - if (k == IND_FOR_REPEAT_EXPANSION_A || k == IND_FOR_REPEAT_EXPANSION_T) { - isIt = true; - break; - } - } - - return isIt; - - } - public static boolean isCGExpansion(VariantContext vc, ReferenceContext ref) { - ArrayList inds = findEventClassificationIndex(vc, ref); - - boolean isIt = false; - for (int k : inds) { - if (k == IND_FOR_REPEAT_EXPANSION_C || k == IND_FOR_REPEAT_EXPANSION_G) { - isIt = true; - break; - } - } - - return isIt; - - } - public static boolean isInsideExtendedIndel(VariantContext vc, ReferenceContext ref) { return (vc.getStart() != ref.getLocus().getStart()); } diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index c4b0165ca..5e3160452 100644 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -237,7 +237,7 @@ public class MathUtils { public static double log10sumLog10(double[] log10p, int start, int finish) { double sum = 0.0; - double maxValue = Utils.findMaxEntry(log10p); + double maxValue = arrayMax(log10p, finish); if(maxValue == Double.NEGATIVE_INFINITY) return sum; @@ -554,7 +554,7 @@ public class MathUtils { // for precision purposes, we need to add (or really subtract, since they're // all negative) the largest value; also, we need to convert to normal-space. - double maxValue = Utils.findMaxEntry(array); + double maxValue = arrayMax(array); // we may decide to just normalize in log space without converting to linear space if (keepInLogSpace) { @@ -627,10 +627,14 @@ public class MathUtils { return maxI; } - public static double arrayMax(double[] array) { + public static double arrayMax(final double[] array) { return array[maxElementIndex(array)]; } + public static double arrayMax(final double[] array, final int endIndex) { + return array[maxElementIndex(array, endIndex)]; + } + public static double arrayMin(double[] array) { return array[minElementIndex(array)]; } diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java index 4817966fe..c2c608903 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java @@ -290,32 +290,6 @@ public class Utils { return m; } - - // returns the maximum value in the array - public static double findMaxEntry(double[] array) { - return findIndexAndMaxEntry(array).first; - } - - // returns the index of the maximum value in the array - public static int findIndexOfMaxEntry(double[] array) { - return findIndexAndMaxEntry(array).second; - } - - // returns the the maximum value and its index in the array - private static Pair findIndexAndMaxEntry(double[] array) { - if ( array.length == 0 ) - return new Pair(0.0, -1); - int index = 0; - double max = array[0]; - for (int i = 1; i < array.length; i++) { - if ( array[i] > max ) { - max = array[i]; - index = i; - } - } - return new Pair(max, index); - } - /** * Splits expressions in command args by spaces and returns the array of expressions. * Expressions may use single or double quotes to group any individual expression, but not both. diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index 2411a7d04..3a5b07e58 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -44,23 +44,24 @@ import java.util.*; public class BaseRecalibration { private QuantizationInfo quantizationInfo; // histogram containing the map for qual quantization (calculated after recalibration is done) private LinkedHashMap> keysAndTablesMap; // quick access reference to the read group table and its key manager - private ArrayList requestedCovariates = new ArrayList(); // list of all covariates to be used in this calculation - private static String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check that needs propagate through the code"; - private static String TOO_MANY_KEYS_EXCEPTION = "There should only be one key for the RG collapsed table, something went wrong here"; /** * Constructor using a GATK Report file * * @param RECAL_FILE a GATK Report file containing the recalibration information */ - public BaseRecalibration(final File RECAL_FILE) { + public BaseRecalibration(final File RECAL_FILE, int quantizationLevels) { RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE); - quantizationInfo = recalibrationReport.getQuantizationInfo(); keysAndTablesMap = recalibrationReport.getKeysAndTablesMap(); requestedCovariates = recalibrationReport.getRequestedCovariates(); + quantizationInfo = recalibrationReport.getQuantizationInfo(); + if (quantizationLevels == 0) // quantizationLevels == 0 means no quantization, preserve the quality scores + quantizationInfo.noQuantization(); + else if (quantizationLevels > 0 && quantizationLevels != quantizationInfo.getQuantizationLevels()) // any other positive value means, we want a different quantization than the one pre-calculated in the recalibration report. Negative values mean the user did not provide a quantization argument, and just wnats to use what's in the report. + quantizationInfo.quantizeQualityScores(quantizationLevels); } /** @@ -71,17 +72,17 @@ public class BaseRecalibration { * @param read the read to recalibrate */ public void recalibrateRead(final GATKSAMRecord read) { - final ReadCovariates readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates); // compute all covariates for the read - for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings + final ReadCovariates readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates); // compute all covariates for the read + for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings final byte[] originalQuals = read.getBaseQualities(errorModel); final byte[] recalQuals = originalQuals.clone(); - for (int offset = 0; offset < read.getReadLength(); offset++) { // recalibrate all bases in the read + for (int offset = 0; offset < read.getReadLength(); offset++) { // recalibrate all bases in the read byte qualityScore = originalQuals[offset]; - if (qualityScore > QualityUtils.MIN_USABLE_Q_SCORE) { // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality) - final BitSet[] keySet = readCovariates.getKeySet(offset, errorModel); // get the keyset for this base using the error model - qualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base + if (qualityScore > QualityUtils.MIN_USABLE_Q_SCORE) { // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality) + final BitSet[] keySet = readCovariates.getKeySet(offset, errorModel); // get the keyset for this base using the error model + qualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base } recalQuals[offset] = qualityScore; } @@ -109,6 +110,9 @@ public class BaseRecalibration { * @return A recalibrated quality score as a byte */ private byte performSequentialQualityCalculation(BitSet[] key, EventType errorModel) { + final String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check that needs propagate through the code"; + final String TOO_MANY_KEYS_EXCEPTION = "There should only be one key for the RG collapsed table, something went wrong here"; + final byte qualFromRead = (byte) BitSetUtils.shortFrom(key[1]); double globalDeltaQ = 0.0; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index 584e76cf9..cbaf705b4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -1202,4 +1202,80 @@ public class VariantContextUtils { final double qual = numNewAltAlleles == 0 ? Genotype.NO_LOG10_PERROR : GenotypeLikelihoods.getQualFromLikelihoods(PLindex, newLikelihoods); return new Genotype(originalGT.getSampleName(), myAlleles, qual, null, attrs, false); } + + /** + * Returns true iff VC is an non-complex indel where every allele represents an expansion or + * contraction of a series of identical bases in the reference. + * + * For example, suppose the ref bases are CTCTCTGA, which includes a 3x repeat of CTCTCT + * + * If VC = -/CT, then this function returns true because the CT insertion matches exactly the + * upcoming reference. + * If VC = -/CTA then this function returns false because the CTA isn't a perfect match + * + * Now consider deletions: + * + * If VC = CT/- then again the same logic applies and this returns true + * The case of CTA/- makes no sense because it doesn't actually match the reference bases. + * + * The logic of this function is pretty simple. Take all of the non-null alleles in VC. For + * each insertion allele of n bases, check if that allele matches the next n reference bases. + * For each deletion allele of n bases, check if this matches the reference bases at n - 2 n, + * as it must necessarily match the first n bases. If this test returns true for all + * alleles you are a tandem repeat, otherwise you are not. + * + * @param vc + * @param refBasesStartingAtVCWithPad not this is assumed to include the PADDED reference + * @return + */ + @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"}) + public static boolean isTandemRepeat(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) { + final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1); + if ( ! vc.isIndel() ) // only indels are tandem repeats + return false; + + final Allele ref = vc.getReference(); + + for ( final Allele allele : vc.getAlternateAlleles() ) { + if ( ! isRepeatAllele(ref, allele, refBasesStartingAtVCWithoutPad) ) + return false; + } + + // we've passed all of the tests, so we are a repeat + return true; + } + + /** + * Helper function for isTandemRepeat that checks that allele matches somewhere on the reference + * @param ref + * @param alt + * @param refBasesStartingAtVCWithoutPad + * @return + */ + protected static boolean isRepeatAllele(final Allele ref, final Allele alt, final String refBasesStartingAtVCWithoutPad) { + if ( ! Allele.oneIsPrefixOfOther(ref, alt) ) + return false; // we require one allele be a prefix of another + + if ( ref.length() > alt.length() ) { // we are a deletion + return basesAreRepeated(ref.getBaseString(), alt.getBaseString(), refBasesStartingAtVCWithoutPad, 2); + } else { // we are an insertion + return basesAreRepeated(alt.getBaseString(), ref.getBaseString(), refBasesStartingAtVCWithoutPad, 1); + } + } + + protected static boolean basesAreRepeated(final String l, final String s, final String ref, final int minNumberOfMatches) { + final String potentialRepeat = l.substring(s.length()); // skip s bases + + for ( int i = 0; i < minNumberOfMatches; i++) { + final int start = i * potentialRepeat.length(); + final int end = (i+1) * potentialRepeat.length(); + if ( ref.length() < end ) + return false; // we ran out of bases to test + final String refSub = ref.substring(start, end); + if ( ! refSub.equals(potentialRepeat) ) + return false; // repeat didn't match, fail + } + + return true; // we passed all tests, we matched + } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index d67fc61e2..035bf4020 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -302,7 +302,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + " --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s", - 1, Arrays.asList("c8a782f51e094dc7be06dbfb795feab2")); + 1, Arrays.asList("4c00cfa0fd343fef62d19af0edeb4f65")); executeTestParallel("testSelect1", spec); } @@ -330,7 +330,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("5c409a2ab4517f862c6678902c0fd7a1")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("4df6654860ad63b7e24e6bc5fbbbcb00")); executeTestParallel("testCompVsEvalAC",spec); } @@ -360,7 +360,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " --dbsnp " + b37dbSNP132 + " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("a27c700eabe6b7b3877c8fd4eabb3975")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("3b85cd0fa37539ff51d34e026f26fef2")); executeTestParallel("testEvalTrackWithoutGenotypes",spec); } @@ -372,7 +372,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("3272a2db627d4f42bc512df49a8ea64b")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("bed8751c773b9568218f78c90f13348a")); executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); } @@ -488,11 +488,32 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("41a37636868a838a632559949c5216cf") + Arrays.asList("9726c0c8f19d271cf680f5f16f0926b3") ); executeTest("testModernVCFWithLargeIndels", spec); } + @Test + public void testStandardIndelEval() { + WalkerTestSpec spec = new WalkerTestSpec( + buildCommandLine( + "-T VariantEval", + "-R " + b37KGReference, + "-eval " + validationDataLocation + "/NA12878.HiSeq.WGS.b37_decoy.indel.recalibrated.vcf", + "-L 20", + "-noST -ST Sample -ST OneBPIndel -ST TandemRepeat", + "-noEV -EV IndelSummary -EV IndelLengthHistogram", + "-gold " + validationDataLocation + "/Mills_and_1000G_gold_standard.indels.b37.sites.vcf", + "-D " + b37dbSNP132, + "-o %s" + ), + 1, + Arrays.asList("c89705147ef4233d5de3a539469bd1d1") + ); + executeTest("testStandardIndelEval", spec); + } + + @Test() public void testIncompatibleEvalAndStrat() { WalkerTestSpec spec = new WalkerTestSpec( diff --git a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java index adc7927a7..5327d4cf2 100755 --- a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java @@ -284,6 +284,18 @@ public class MathUtilsUnitTest extends BaseTest { Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[] {-1.0, -3.0, -1.0, -2.0}), new double[] {0.1 * 1.0 / 0.211, 0.001 * 1.0 / 0.211, 0.1 * 1.0 / 0.211, 0.01 * 1.0 / 0.211})); } + @Test + public void testLog10sumLog10() { + final double log3 = 0.477121254719662; + Assert.assertEquals(MathUtils.compareDoubles(MathUtils.log10sumLog10(new double[]{0.0, 0.0, 0.0}), log3), 0); + Assert.assertEquals(MathUtils.compareDoubles(MathUtils.log10sumLog10(new double[] {0.0, 0.0, 0.0}, 0), log3), 0); + Assert.assertEquals(MathUtils.compareDoubles(MathUtils.log10sumLog10(new double[]{0.0, 0.0, 0.0}, 0, 3), log3), 0); + + final double log2 = 0.301029995663981; + Assert.assertEquals(MathUtils.compareDoubles(MathUtils.log10sumLog10(new double[] {0.0, 0.0, 0.0}, 0, 2), log2), 0); + Assert.assertEquals(MathUtils.compareDoubles(MathUtils.log10sumLog10(new double[] {0.0, 0.0, 0.0}, 0, 1), 0.0), 0); + } + @Test public void testDotProduct() { Assert.assertEquals(MathUtils.dotProduct(new Double[]{-5.0,-3.0,2.0}, new Double[]{6.0,7.0,8.0}),-35.0,1e-3); diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/BaseRecalibrationUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/BaseRecalibrationUnitTest.java index a372ef3f0..f8f1ead9b 100644 --- a/public/java/test/org/broadinstitute/sting/utils/recalibration/BaseRecalibrationUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/BaseRecalibrationUnitTest.java @@ -20,7 +20,7 @@ public class BaseRecalibrationUnitTest { @Test(enabled=false) public void testReadingReport() { File csv = new File("public/testdata/exampleGATKREPORT.grp"); - BaseRecalibration baseRecalibration = new BaseRecalibration(csv); + BaseRecalibration baseRecalibration = new BaseRecalibration(csv, -1); GATKSAMRecord read = ReadUtils.createRandomRead(1000); read.setReadGroup(new GATKSAMReadGroupRecord(new SAMReadGroupRecord("exampleBAM.bam.bam"), NGSPlatform.ILLUMINA)); baseRecalibration.recalibrateRead(read); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index ccf560f83..107241beb 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -589,4 +589,76 @@ public class VariantContextUtilsUnitTest extends BaseTest { return priority; } + + + // -------------------------------------------------------------------------------- + // + // Test repeats + // + // -------------------------------------------------------------------------------- + + private class RepeatDetectorTest extends TestDataProvider { + String ref; + boolean isTrueRepeat; + VariantContext vc; + + private RepeatDetectorTest(boolean isTrueRepeat, String ref, String refAlleleString, String ... altAlleleStrings) { + super(RepeatDetectorTest.class); + this.ref = "N" + ref; // add a dummy base for the event here + this.isTrueRepeat = isTrueRepeat; + + List alleles = new LinkedList(); + final Allele refAllele = Allele.create(refAlleleString, true); + alleles.add(refAllele); + for ( final String altString: altAlleleStrings) { + final Allele alt = Allele.create(altString, false); + alleles.add(alt); + } + + VariantContextBuilder builder = new VariantContextBuilder("test", "chr1", 1, 1 + refAllele.length(), alleles); + this.vc = builder.make(); + } + + public String toString() { + return String.format("%s refBases=%s trueRepeat=%b vc=%s", super.toString(), ref, isTrueRepeat, vc); + } + } + + @DataProvider(name = "RepeatDetectorTest") + public Object[][] makeRepeatDetectorTest() { + new RepeatDetectorTest(true, "AAC", "-", "A"); + new RepeatDetectorTest(true, "AAC", "A", "-"); + new RepeatDetectorTest(false, "AAC", "AA", "-"); + new RepeatDetectorTest(false, "AAC", "-", "C"); + new RepeatDetectorTest(false, "AAC", "A", "C"); + + // running out of ref bases => false + new RepeatDetectorTest(false, "AAC", "-", "CAGTA"); + + // complex repeats + new RepeatDetectorTest(true, "ATATATC", "-", "AT"); + new RepeatDetectorTest(true, "ATATATC", "-", "ATA"); + new RepeatDetectorTest(true, "ATATATC", "-", "ATAT"); + new RepeatDetectorTest(true, "ATATATC", "AT", "-"); + new RepeatDetectorTest(false, "ATATATC", "ATA", "-"); + new RepeatDetectorTest(false, "ATATATC", "ATAT", "-"); + + // multi-allelic + new RepeatDetectorTest(true, "ATATATC", "-", "AT", "ATAT"); + new RepeatDetectorTest(true, "ATATATC", "-", "AT", "ATA"); + new RepeatDetectorTest(true, "ATATATC", "AT", "-", "ATAT"); + new RepeatDetectorTest(true, "ATATATC", "AT", "-", "ATA"); // two As + new RepeatDetectorTest(false, "ATATATC", "AT", "-", "ATC"); // false + new RepeatDetectorTest(false, "ATATATC", "AT", "-", "CC"); // false + new RepeatDetectorTest(false, "ATATATC", "AT", "ATAT", "CC"); // false + + return RepeatDetectorTest.getTests(RepeatDetectorTest.class); + } + + @Test(dataProvider = "RepeatDetectorTest") + public void testRepeatDetectorTest(RepeatDetectorTest cfg) { + + // test alleles are equal + Assert.assertEquals(VariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat); + } } diff --git a/public/testdata/exampleGRP.grp b/public/testdata/exampleGRP.grp index 492d9f05d..67a39dc3a 100644 --- a/public/testdata/exampleGRP.grp +++ b/public/testdata/exampleGRP.grp @@ -118,1401 +118,1401 @@ QualityScore Count QuantizedScore #:GATKTable:false:6:3:%s:%s:%.4f:%.4f:%d:%d:; #:GATKTable:RecalTable0: ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors -exampleBAM.bam.bam D 25.8092 3.0332 380 0 -exampleBAM.bam.bam M 14.0483 3.0403 380 14 -exampleBAM.bam.bam I 25.8092 3.0332 380 0 +exampleBAM.bam.bam D 25.8092 45.0000 380 0 +exampleBAM.bam.bam M 14.0483 15.4820 380 14 +exampleBAM.bam.bam I 25.8092 45.0000 380 0 -#:GATKTable:false:7:32:%s:%s:%s:%.4f:%.4f:%d:%d:; +#:GATKTable:false:6:32:%s:%s:%s:%.4f:%d:%d:; #:GATKTable:RecalTable1: -ReadGroup QualityScore EventType EmpiricalQuality EstimatedQReported Observations Errors -exampleBAM.bam.bam 32 M 15.1851 3.2902 32 0 -exampleBAM.bam.bam 19 M 9.0309 2.7369 15 1 -exampleBAM.bam.bam 33 M 15.5630 2.8881 35 0 -exampleBAM.bam.bam 18 M 6.0206 2.4476 7 1 -exampleBAM.bam.bam 34 M 15.6820 3.2583 36 0 -exampleBAM.bam.bam 17 M 5.4407 4.6854 6 1 -exampleBAM.bam.bam 16 M 7.4036 3.9252 10 1 -exampleBAM.bam.bam 23 M 12.0412 2.7327 15 0 -exampleBAM.bam.bam 6 M 4.7712 2.8181 11 3 -exampleBAM.bam.bam 45 I 25.8092 3.0332 380 0 -exampleBAM.bam.bam 22 M 10.0000 2.5582 9 0 -exampleBAM.bam.bam 4 M 4.7712 2.8368 5 1 -exampleBAM.bam.bam 21 M 12.5527 2.7659 17 0 -exampleBAM.bam.bam 5 M 4.2597 2.7881 7 2 -exampleBAM.bam.bam 20 M 4.7712 2.2330 5 1 -exampleBAM.bam.bam 27 M 13.6173 3.4225 22 0 -exampleBAM.bam.bam 10 M 3.0103 0.4576 1 0 -exampleBAM.bam.bam 26 M 8.4510 4.7603 6 0 -exampleBAM.bam.bam 11 M 1.7609 11.0000 2 1 -exampleBAM.bam.bam 8 M 6.0206 2.6060 7 1 -exampleBAM.bam.bam 25 M 12.0412 2.7317 15 0 -exampleBAM.bam.bam 9 M 6.9897 5.0453 4 0 -exampleBAM.bam.bam 24 M 10.2119 3.4640 20 1 -exampleBAM.bam.bam 31 M 14.1497 2.8402 25 0 -exampleBAM.bam.bam 14 M 3.0103 0.1764 1 0 -exampleBAM.bam.bam 30 M 13.2222 3.4669 20 0 -exampleBAM.bam.bam 15 M 7.7815 2.2645 5 0 -exampleBAM.bam.bam 12 M 6.9897 5.5045 4 0 -exampleBAM.bam.bam 29 M 13.2222 3.4667 20 0 -exampleBAM.bam.bam 45 D 25.8092 3.0332 380 0 -exampleBAM.bam.bam 13 M 6.0206 1.8711 3 0 -exampleBAM.bam.bam 28 M 12.0412 2.7309 15 0 +ReadGroup QualityScore EventType EmpiricalQuality Observations Errors +exampleBAM.bam.bam 32 M 15.1851 32 0 +exampleBAM.bam.bam 19 M 9.0309 15 1 +exampleBAM.bam.bam 33 M 15.5630 35 0 +exampleBAM.bam.bam 18 M 6.0206 7 1 +exampleBAM.bam.bam 34 M 15.6820 36 0 +exampleBAM.bam.bam 17 M 5.4407 6 1 +exampleBAM.bam.bam 16 M 7.4036 10 1 +exampleBAM.bam.bam 23 M 12.0412 15 0 +exampleBAM.bam.bam 6 M 4.7712 11 3 +exampleBAM.bam.bam 45 I 25.8092 380 0 +exampleBAM.bam.bam 22 M 10.0000 9 0 +exampleBAM.bam.bam 4 M 4.7712 5 1 +exampleBAM.bam.bam 21 M 12.5527 17 0 +exampleBAM.bam.bam 5 M 4.2597 7 2 +exampleBAM.bam.bam 20 M 4.7712 5 1 +exampleBAM.bam.bam 27 M 13.6173 22 0 +exampleBAM.bam.bam 10 M 3.0103 1 0 +exampleBAM.bam.bam 26 M 8.4510 6 0 +exampleBAM.bam.bam 11 M 1.7609 2 1 +exampleBAM.bam.bam 8 M 6.0206 7 1 +exampleBAM.bam.bam 25 M 12.0412 15 0 +exampleBAM.bam.bam 9 M 6.9897 4 0 +exampleBAM.bam.bam 24 M 10.2119 20 1 +exampleBAM.bam.bam 31 M 14.1497 25 0 +exampleBAM.bam.bam 14 M 3.0103 1 0 +exampleBAM.bam.bam 30 M 13.2222 20 0 +exampleBAM.bam.bam 15 M 7.7815 5 0 +exampleBAM.bam.bam 12 M 6.9897 4 0 +exampleBAM.bam.bam 29 M 13.2222 20 0 +exampleBAM.bam.bam 45 D 25.8092 380 0 +exampleBAM.bam.bam 13 M 6.0206 3 0 +exampleBAM.bam.bam 28 M 12.0412 15 0 -#:GATKTable:false:9:1354:%s:%s:%s:%s:%s:%.4f:%.4f:%d:%d:; +#:GATKTable:false:8:1354:%s:%s:%s:%s:%s:%.4f:%d:%d:; #:GATKTable:RecalTable2: -ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality EstimatedQReported Observations Errors -exampleBAM.bam.bam 45 TGAAAGTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGTATTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGCCTCGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTGTGTCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTTGTAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTAAGTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTTATTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 23 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 27 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ATTCTATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTAATCTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 GC Context M 4.7712 34.0000 2 0 -exampleBAM.bam.bam 8 TG Context M 6.0206 2.1195 3 0 -exampleBAM.bam.bam 45 TAGAGTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 9 TA Context M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 45 GGTTCGGG Context I 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 AGTTTCAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CATTTCAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 7 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 5 76 Cycle M 3.0103 1.6509 1 0 -exampleBAM.bam.bam 45 CATGATAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 53 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 57 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 25 52 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 45 TGGCAGCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 CT Context M 8.4510 4.7690 6 0 -exampleBAM.bam.bam 45 AAGTGACA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGTGACAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGAGTTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTCTTTGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCCTGAAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 12 25 Cycle M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 34 75 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 32 41 Cycle M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 21 GG Context M 4.7712 21.0000 2 0 -exampleBAM.bam.bam 26 50 Cycle M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 ACCTGGAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACAGCAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 20 GA Context M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 45 AGGTGGAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCAAAATC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 27 TA Context M 6.9897 6.0033 4 0 -exampleBAM.bam.bam 27 18 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 32 CC Context M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 45 AAAATCTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 22 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 26 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 33 76 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 30 24 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TTCTATTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTCAATGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 21 73 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 17 4 Cycle M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 8 17 Cycle M 3.0103 0.7494 1 0 -exampleBAM.bam.bam 34 GA Context M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 ATCGTGAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCAGATCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GATCGTGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 52 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 56 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 9 TC Context M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 23 CT Context M 4.7712 23.0000 2 0 -exampleBAM.bam.bam 31 26 Cycle M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 45 ATGTGAAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTACTCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACACAGCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 26 TT Context M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 GGGTTTGG Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 33 8 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 21 GT Context M 4.7712 21.0000 2 0 -exampleBAM.bam.bam 34 74 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 ATTCTTAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GAGCCTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 20 GC Context M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 45 GGTTAGGG Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 33 42 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 GTGCAAAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 6 75 Cycle M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 27 TC Context M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 32 CA Context M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 29 60 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 34 13 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 34 GT Context M 4.7712 34.0000 2 0 -exampleBAM.bam.bam 21 74 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 GTTAATGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TATTATTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 52 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 CTTTCAGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GACATGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATCATGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 21 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 25 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 34 47 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 31 25 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 19 71 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 6 GG Context M 3.9794 4.2528 4 1 -exampleBAM.bam.bam 9 16 Cycle M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 45 TCCAGTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCACATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAAGTGAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGACATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 55 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 59 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CATGATCG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 AT Context M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 32 43 Cycle M 6.0206 1.7623 3 0 -exampleBAM.bam.bam 19 33 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 21 GA Context M 4.7712 21.0000 2 0 -exampleBAM.bam.bam 45 GTATTTGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 26 TA Context M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 TCTTAAGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 CC Context M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 11 20 Cycle M 3.0103 0.3594 1 0 -exampleBAM.bam.bam 28 61 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 18 1 Cycle M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 45 ACCCAGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AAAGACAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCCTTTGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 27 16 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 27 TG Context M 4.7712 27.0000 2 0 -exampleBAM.bam.bam 32 CT Context M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 21 44 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TATTACTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGGCTGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 65 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 34 GG Context M 4.7712 34.0000 2 0 -exampleBAM.bam.bam 25 21 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 22 9 Cycle M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 CAGGCCAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 20 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 24 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 30 26 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TTGTATTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 53 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 23 CC Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 19 70 Cycle M -0.0000 0.0550 1 1 -exampleBAM.bam.bam 25 55 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 45 AGGCCACC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 54 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 58 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ACTTTCAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AAAGTGCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTGATAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATGTGAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 9 TT Context M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 19 32 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 29 28 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 45 CGGGTTTG Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 TCTTTGTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 10 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 33 CA Context M 4.7712 33.0000 2 0 -exampleBAM.bam.bam 45 GTTCGGGT Context I 6.0206 1.7610 3 0 -exampleBAM.bam.bam 27 TT Context M 4.7712 27.0000 2 0 -exampleBAM.bam.bam 27 17 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 45 CAGCAAAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGCAGCCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 20 GT Context M -0.0000 0.0436 1 1 -exampleBAM.bam.bam 45 TGGAGCCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGTGGCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 30 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 33 40 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 24 TG Context M 4.7712 24.0000 2 0 -exampleBAM.bam.bam 45 TGTGTCTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCAATAAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTCCAGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 49 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 61 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CCTCGTCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGCACCCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 44 Cycle M 4.7712 22.0000 2 0 -exampleBAM.bam.bam 45 AGGTTATC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 41 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 19 65 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 23 12 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 23 GG Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 45 TTGGGTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCTGTGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGTTGGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 50 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 GTTTCACA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCGGGTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAGGGTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 73 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 9 52 Cycle M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 45 19 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 31 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 25 TA Context M 6.0206 1.7678 3 0 -exampleBAM.bam.bam 34 11 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 34 CC Context M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 28 25 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 TAGATTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTTGGGG Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 GGCTGGGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GATTAGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 5 GG Context M 3.0103 2.5084 3 1 -exampleBAM.bam.bam 32 15 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 27 22 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 21 42 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 19 5 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 19 AT Context M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 45 TTTCAGGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGCCAGGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTCTTTAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGAACTGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 26 20 Cycle M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 TATTCTTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGATAACC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTTTTCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGCTTTAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 5 46 Cycle M -0.0000 1.6509 1 1 -exampleBAM.bam.bam 29 27 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 45 ATCCATTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 48 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 60 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GATCCAGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATGAGTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 TT Context M 3.0103 1.7696 3 1 -exampleBAM.bam.bam 45 TCTTTATA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 6 CC Context M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 23 GT Context M 4.7712 23.0000 2 0 -exampleBAM.bam.bam 34 40 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 18 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 30 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CAAAATCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 15 Cycle M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 CCAGGTTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCATGGTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTAATCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGGTTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAGGGTTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTGGTTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 72 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 31 60 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 34 CA Context M 6.9897 6.0171 4 0 -exampleBAM.bam.bam 45 CCCAGATC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 18 36 Cycle M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 16 70 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 45 TGTATTTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 46 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 GGTTGGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTTGGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCTAGAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 19 AG Context M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 32 GA Context M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 32 14 Cycle M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 12 62 Cycle M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 33 12 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 GGTGGCCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 4 GC Context M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 27 53 Cycle M 4.7712 27.0000 2 0 -exampleBAM.bam.bam 23 GA Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 45 TTATTATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 5 74 Cycle M 3.0103 1.6509 1 0 -exampleBAM.bam.bam 45 ATGATAAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 51 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 63 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CACCCAGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CGTGAGTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCTTTATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATGGTGGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 CT Context M 4.7712 34.0000 2 0 -exampleBAM.bam.bam 4 72 Cycle M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 45 TCGGGTTT Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 24 48 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 TCCATGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACATGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 17 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 29 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ATCAATAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACCATGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 GT Context M 8.4510 4.7685 6 0 -exampleBAM.bam.bam 19 7 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 33 45 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 28 27 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 TCCATTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GATAACCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AACTGGGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 4 GG Context M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 33 GC Context M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TCAGGCCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGCACTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCACTGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTCCAGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 6 CT Context M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 23 15 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 25 51 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 32 72 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 34 42 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 GATATAAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTAGAGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 50 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 62 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GCCACCAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGGTTCGG Context D 6.0206 1.7610 3 0 -exampleBAM.bam.bam 24 TC Context M 6.0206 1.7696 3 0 -exampleBAM.bam.bam 25 TT Context M 4.7712 25.0000 2 0 -exampleBAM.bam.bam 45 16 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 28 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ACATGGTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 34 Cycle M -0.0000 0.1105 1 1 -exampleBAM.bam.bam 45 AATCTCCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTTCACT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 GT Context M 4.7712 22.0000 2 0 -exampleBAM.bam.bam 45 ATATCAAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAATGTGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GAGTCAAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 49 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 GGGGGTTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAGGGTTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGCAATCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGGGTTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTAATGAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 30 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 23 75 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 32 GG Context M 7.7815 2.2194 5 0 -exampleBAM.bam.bam 20 9 Cycle M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 20 CT Context M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 45 ATTAGATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 44 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TTTCTGTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGAGATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTTGGGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 21 11 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 29 24 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 32 46 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 27 55 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 45 ATATAAAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GAGTTTCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACTTTCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCATTTCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCAGGCAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 11 TT Context M -0.0000 0.3594 1 1 -exampleBAM.bam.bam 45 TTTCACTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 GA Context M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TCGTGAGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TACTCTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAATGAGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGTCTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGCTTTAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 70 Cycle M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 ATTTTTCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGCCAGGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 1 Cycle M 4.7712 33.0000 2 0 -exampleBAM.bam.bam 45 TTTCAGGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TATTCTTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGATAACC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTCTTTAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGAACTGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 21 AG Context M 4.7712 21.0000 2 0 -exampleBAM.bam.bam 32 33 Cycle M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 27 56 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 45 GGCTGGGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GATTAGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 35 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TAGATTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTTGGGG Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 19 CT Context M 1.7609 19.0000 2 1 -exampleBAM.bam.bam 45 19 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 31 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 TGTTGGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCTGTGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 62 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 TCGGGTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTTCACA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAGGGTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGGTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 TT Context M 4.7712 30.0000 2 0 -exampleBAM.bam.bam 30 17 Cycle M 4.7712 30.0000 2 0 -exampleBAM.bam.bam 33 69 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 6 36 Cycle M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 17 GT Context M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 21 64 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 34 AC Context M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 16 GC Context M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 45 CCTCGTCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 49 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 61 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGGTTATC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGCACCCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGTGTCTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCAATAAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTCCAGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 6 AA Context M 4.7712 6.0000 2 0 -exampleBAM.bam.bam 31 TC Context M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 31 19 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 8 58 Cycle M 3.0103 0.7494 1 0 -exampleBAM.bam.bam 28 54 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 GGTGGCCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 18 10 Cycle M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 18 CA Context M 4.7712 18.0000 2 0 -exampleBAM.bam.bam 27 57 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 21 AT Context M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TGTATTTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCTAGAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTTGGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTTGGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 13 TA Context M 3.0103 0.2233 1 0 -exampleBAM.bam.bam 20 AC Context M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 45 CCCAGATC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 2 Cycle M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 27 27 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 6 67 Cycle M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 45 TAGGGTTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTGGTTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCATGGTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTAATCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGGTTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 TG Context M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 18 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 30 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CCAGGTTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAAAATCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 25 31 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 34 6 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 34 AA Context M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 17 GG Context M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 23 35 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 45 TCTTTATA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GATCCAGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 48 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 60 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ATCCATTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATGAGTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 31 TA Context M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 21 AA Context M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 34 65 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 CTCCAGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 18 CT Context M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 33 3 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TCAGGCCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGCACTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 53 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 TTCACTGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 19 CC Context M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 32 1 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 45 GATAACCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AACTGGGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 73 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 45 TCCATTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 21 66 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 34 5 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 34 AT Context M 8.4510 4.7695 6 0 -exampleBAM.bam.bam 16 47 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 45 CACATGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 17 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 29 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ATCAATAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACCATGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCGGGTTT Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 TCCATGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 6 AG Context M -0.0000 1.2563 1 1 -exampleBAM.bam.bam 6 4 Cycle M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 31 TT Context M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 45 ATGATAAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 51 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 63 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CGTGAGTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACCCAGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 GT Context M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 5 70 Cycle M 3.0103 1.6509 1 0 -exampleBAM.bam.bam 45 GCTTTATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATGGTGGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTATTATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 64 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 21 AC Context M 6.0206 1.7782 3 0 -exampleBAM.bam.bam 33 2 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TTTCACTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCGTGAGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGTCTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAATGAGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TACTCTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACTTTCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCATTTCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATATAAAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GAGTTTCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCAGGCAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 29 54 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 6 65 Cycle M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 19 10 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 19 CA Context M 4.7712 19.0000 2 0 -exampleBAM.bam.bam 45 TTTCTGTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 32 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 GTTTGGGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGAGATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTAGATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 4 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 21 67 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TGGGGTTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGCAATCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGGGGTTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAGGGTTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTAATGAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 18 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 30 TA Context M 6.9897 6.0119 4 0 -exampleBAM.bam.bam 45 16 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 28 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ACATGGTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GAGTCAAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAATGTGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATCTCCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTTCACT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATATCAAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 8 57 Cycle M -0.0000 0.7494 1 1 -exampleBAM.bam.bam 34 38 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 31 16 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 31 TG Context M 6.0206 1.7626 3 0 -exampleBAM.bam.bam 45 GGGTTCGG Context I 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 CTAGAGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 50 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 62 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GATATAAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCCACCAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACCTGGAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 5 AG Context M 3.0103 1.6509 1 0 -exampleBAM.bam.bam 45 AGGTGGAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCAAAATC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACAGCAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 TT Context M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 33 39 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 19 GT Context M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 23 64 Cycle M 4.7712 23.0000 2 0 -exampleBAM.bam.bam 27 30 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 32 AC Context M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 45 AAGTGACA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 5 38 Cycle M 3.0103 1.6509 1 0 -exampleBAM.bam.bam 45 AGAGTTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGTGACAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCCTGAAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTCTTTGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 AT Context M 4.7712 33.0000 2 0 -exampleBAM.bam.bam 45 TGGCAGCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 4 AA Context M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 29 TC Context M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 34 71 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 AGTTTCAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CATTTCAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 53 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 57 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CATGATAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAGAGTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTTCGGG Context D 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 CTTTATTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTTGTAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGCCTCGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTGTGTCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTAAGTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTCTATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTAATCTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 23 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 27 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 30 21 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TGAAAGTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGTATTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 23 38 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 34 3 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 GGTTAGGG Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 GTGCAAAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 TG Context M 6.0206 1.7644 3 0 -exampleBAM.bam.bam 45 ATTCTTAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GAGCCTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 27 31 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 29 48 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 32 AA Context M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 19 GG Context M 4.7712 19.0000 2 0 -exampleBAM.bam.bam 4 37 Cycle M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 45 GGGTTTGG Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 33 AG Context M 6.0206 1.7620 3 0 -exampleBAM.bam.bam 28 50 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 ATTACTCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACACAGCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATGTGAAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 36 Cycle M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 29 TA Context M 4.7712 29.0000 2 0 -exampleBAM.bam.bam 34 70 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 17 76 Cycle M -0.0000 0.0875 1 1 -exampleBAM.bam.bam 30 54 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 24 25 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 ATCGTGAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GATCGTGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 52 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 56 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CCAGATCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 CA Context M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 8 63 Cycle M 3.0103 0.7494 1 0 -exampleBAM.bam.bam 14 TG Context M 3.0103 0.1764 1 0 -exampleBAM.bam.bam 23 AT Context M 6.0206 1.7718 3 0 -exampleBAM.bam.bam 19 72 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 30 20 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TTCTATTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTCAATGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AAAATCTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 22 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 26 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 34 2 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 19 GC Context M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 6 68 Cycle M -0.0000 1.2563 1 1 -exampleBAM.bam.bam 23 66 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 27 28 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 32 AT Context M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 5 AA Context M 3.0103 1.6509 1 0 -exampleBAM.bam.bam 45 TATTACTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 37 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TGGGCTGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 TC Context M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 4 AG Context M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 29 TT Context M 4.7712 29.0000 2 0 -exampleBAM.bam.bam 18 GT Context M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 45 AAAGACAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCCTTTGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACCCAGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTTAAGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 13 55 Cycle M 3.0103 0.2233 1 0 -exampleBAM.bam.bam 45 GTATTTGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 7 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 33 AC Context M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 23 AA Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 8 60 Cycle M 3.0103 0.7494 1 0 -exampleBAM.bam.bam 22 38 Cycle M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 CATGATCG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 55 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 59 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 TCCAGTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGACATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCACATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAAGTGAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 4 64 Cycle M -0.0000 2.2048 1 1 -exampleBAM.bam.bam 25 24 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 22 AG Context M 4.7712 22.0000 2 0 -exampleBAM.bam.bam 45 CTTTCAGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATCATGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 21 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 25 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GACATGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 23 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 33 67 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 24 56 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 TATTATTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTAATGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 AG Context M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 23 67 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 45 TGGAGCCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGTGGCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 TA Context M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 CAGCAAAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGCAGCCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 68 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 21 3 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TCTTTGTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTCGGGT Context D 6.0206 1.7610 3 0 -exampleBAM.bam.bam 28 48 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 33 AA Context M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 18 GG Context M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 45 CGGGTTTG Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 34 34 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 23 AC Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 30 52 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 24 27 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 AGGCCACC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 20 69 Cycle M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 45 AAAGTGCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTGATAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATGTGAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 54 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 58 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ACTTTCAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 23 37 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 21 71 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 33 66 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 15 TG Context M 3.0103 0.1396 1 0 -exampleBAM.bam.bam 45 TTGTATTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 20 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 24 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CAGGCCAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 23 59 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 17 20 Cycle M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 30 CG Context M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TTGATATA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCTTAAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 15 14 Cycle M 3.0103 0.1396 1 0 -exampleBAM.bam.bam 45 GAACTGGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 6 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 10 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GGGCTGGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 31 10 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 34 60 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 25 37 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 6 31 Cycle M -0.0000 1.2563 1 1 -exampleBAM.bam.bam 30 42 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 GTTCTAGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TATTTGCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 5 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 CCTTTGCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGGCACC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 36 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 40 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 29 GA Context M 4.7712 29.0000 2 0 -exampleBAM.bam.bam 21 29 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TAATCTCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 15 74 Cycle M 3.0103 0.1396 1 0 -exampleBAM.bam.bam 45 TTGGGGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 24 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 GTTGGGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCTGGGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 66 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CTTGGCTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGCCACCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 19 TG Context M 4.7712 19.0000 2 0 -exampleBAM.bam.bam 45 TTCAGGCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTTAATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTGGAGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 GG Context M 6.0206 1.7644 3 0 -exampleBAM.bam.bam 45 GAGATTAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 7 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 11 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 TTACTCTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 9 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TTTATATC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGTTAAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTATTACT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 31 11 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 31 CC Context M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 34 61 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 25 36 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 45 ACAGCAAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGTGCAAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 37 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 41 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 TCCAGGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGAGTGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTATCATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 AG Context M 4.7712 24.0000 2 0 -exampleBAM.bam.bam 29 GC Context M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 32 57 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 45 67 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 18 19 Cycle M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 45 CTGGAGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGATTTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AAATCTAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTGAAAGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGCACCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTGTGTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGGCTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 47 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 GTTGGGGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 19 TT Context M 4.7712 19.0000 2 0 -exampleBAM.bam.bam 29 45 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 45 CCTGGAGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATGATTCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCCAGGCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTATTAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 59 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TCTATTCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAACCTGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 CA Context M 6.0206 1.7631 3 0 -exampleBAM.bam.bam 15 GG Context M 4.7712 15.0000 2 0 -exampleBAM.bam.bam 45 GACACAGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AACCTGGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 4 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 8 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 25 AT Context M 4.7712 25.0000 2 0 -exampleBAM.bam.bam 6 63 Cycle M 4.7712 6.0000 2 0 -exampleBAM.bam.bam 45 TTTGCAAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTGCACT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTAAGTGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGAGTCAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 59 Cycle M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 CTCGTCCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 38 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 42 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 34 62 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 31 CG Context M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 31 8 Cycle M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 27 69 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 26 3 Cycle M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 TATAAAGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGGGTTGG Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 64 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 76 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GATTCTAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGACACAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGGTTGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGTGTTGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 29 12 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 29 GG Context M 6.9897 6.0097 4 0 -exampleBAM.bam.bam 8 71 Cycle M 3.0103 0.7494 1 0 -exampleBAM.bam.bam 45 GTGAACTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGCTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 9 69 Cycle M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 45 CCTGAAAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTTGCAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 20 29 Cycle M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 12 40 Cycle M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 32 24 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 21 61 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 CATGGTAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCACCCAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 55 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 45 ATGATCGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 5 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 9 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 30 CC Context M 4.7712 30.0000 2 0 -exampleBAM.bam.bam 23 56 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 6 62 Cycle M 3.0103 1.2563 1 0 -exampleBAM.bam.bam 31 43 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 25 AG Context M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 45 ATAACCTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 39 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 43 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GAAAGTGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 AA Context M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 24 6 Cycle M 4.7712 24.0000 2 0 -exampleBAM.bam.bam 45 TTATTGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 63 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 31 CT Context M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 45 65 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 18 TT Context M -0.0000 0.0694 1 1 -exampleBAM.bam.bam 45 GATTTTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGTTCTAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TAAAGACA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGAGTGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTCACAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGGAGCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 19 49 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 29 GT Context M 4.7712 29.0000 2 0 -exampleBAM.bam.bam 5 26 Cycle M -0.0000 1.6509 1 1 -exampleBAM.bam.bam 45 AAGTGCAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTTGCAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATCTAATC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 20 28 Cycle M -0.0000 0.0436 1 1 -exampleBAM.bam.bam 45 GGTATTAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGTGAACT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGCCTGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 57 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 21 60 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 29 47 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 34 56 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 31 GA Context M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 45 TCGTCCAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGATTCTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATCCAGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 32 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 44 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CATGATTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAATCCAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGTTCTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 26 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 8 AT Context M -0.0000 0.7494 1 1 -exampleBAM.bam.bam 45 GGGTTAGG Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 30 12 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TATATCAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCAATCCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGAGCCTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGATCCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 2 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 14 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GAGTGTTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 30 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 27 AC Context M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 21 59 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TGTCTTTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCAATGTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGCTTTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 13 GA Context M 3.0103 0.2233 1 0 -exampleBAM.bam.bam 45 CCATGATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 29 CA Context M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 19 54 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 45 TATCAATA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTGGGCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGTTAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGCACTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTAGAGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 26 AT Context M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 20 57 Cycle M 3.0103 0.0436 1 0 -exampleBAM.bam.bam 45 GCCTCGTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 70 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 74 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 18 22 Cycle M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 25 32 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 27 66 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 31 15 Cycle M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 31 GC Context M 6.0206 1.7626 3 0 -exampleBAM.bam.bam 45 33 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 45 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GGAGATTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGATCCAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 19 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 45 ATGGTATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATCTCCAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 13 75 Cycle M 3.0103 0.2233 1 0 -exampleBAM.bam.bam 45 TTTGTATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TATCATGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGACATGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 17 TT Context M 3.0103 1.8045 3 1 -exampleBAM.bam.bam 31 45 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 8 AG Context M 4.7712 8.0000 2 0 -exampleBAM.bam.bam 34 27 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 3 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 15 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 TTATATCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGATATAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTTATCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCACTGAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGGCCTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 19 21 Cycle M 4.7712 19.0000 2 0 -exampleBAM.bam.bam 32 31 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 27 AA Context M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 45 CACTGATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATAAAGAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCACTTTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGCCTCG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 CT Context M 4.7712 28.0000 2 0 -exampleBAM.bam.bam 45 71 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 75 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGCAAAAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGCAATC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 29 Cycle M 4.7712 33.0000 2 0 -exampleBAM.bam.bam 26 AG Context M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 GGTTTGGG Context D 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 GGGTTGGG Context D 6.0206 1.7610 3 0 -exampleBAM.bam.bam 24 3 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 TTTTTCTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTAGATTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 16 TG Context M 4.7712 16.0000 2 0 -exampleBAM.bam.bam 45 34 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 46 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ATGAGTCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 27 65 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 31 12 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 31 GG Context M 6.9897 6.0137 4 0 -exampleBAM.bam.bam 34 58 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 24 33 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 15 8 Cycle M 3.0103 0.1396 1 0 -exampleBAM.bam.bam 26 67 Cycle M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 30 GA Context M 4.7712 30.0000 2 0 -exampleBAM.bam.bam 45 12 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GGCCTGAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGATTAGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCAGCCTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CATGGTGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATCCATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTTATAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 29 76 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 23 61 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 28 CA Context M 4.7712 28.0000 2 0 -exampleBAM.bam.bam 45 GTTAGGGT Context I 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 ACTCTTTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGCCTTTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACATGATC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTATTGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 28 Cycle M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 29 42 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 27 AT Context M 6.9897 6.0033 4 0 -exampleBAM.bam.bam 45 TGGGTTAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGGTTCG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 26 7 Cycle M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 TTTTCTGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGGTTAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGGTTCG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CGGGTTCG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 68 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 72 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGTCAATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 29 8 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 29 CG Context M 4.7712 29.0000 2 0 -exampleBAM.bam.bam 4 29 Cycle M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 16 TT Context M 3.9794 5.8077 4 1 -exampleBAM.bam.bam 45 CACCATGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 35 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 47 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CTATTCTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATCTAAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGTTGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 45 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TCACATGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 9 AG Context M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 45 GTCCATGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 31 13 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 31 GT Context M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 34 59 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 AAGACACA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCACCATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 1 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 13 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 16 51 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 45 CGTCCATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTGGGGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTGGGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCGGGTT Context I 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 TTAGGGTT Context I 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 TGGGGGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTGGGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGGGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 9 38 Cycle M 3.0103 0.5844 1 0 -exampleBAM.bam.bam 45 GTTATCAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 GC Context M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 17 TC Context M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 34 25 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 CCATGATA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 11 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 TATTGATA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 29 43 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 45 CCAGTTCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGGTTAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 69 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 73 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 28 41 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 33 31 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TGATCGTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 29 9 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 12 GC Context M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 29 6 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 45 GCCTCGTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 70 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 74 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 TTTGGGCT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TATCAATA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 TG Context M 6.0206 1.7620 3 0 -exampleBAM.bam.bam 45 TTGGTTAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTAGAGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGCACTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 4 49 Cycle M 3.0103 2.2048 1 0 -exampleBAM.bam.bam 32 18 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 10 GT Context M 3.0103 0.4576 1 0 -exampleBAM.bam.bam 27 11 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 27 CC Context M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 45 CCATGATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 5 TT Context M 1.7609 5.0000 2 1 -exampleBAM.bam.bam 18 56 Cycle M 3.0103 0.0694 1 0 -exampleBAM.bam.bam 45 TGGCTTTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGTCTTTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCAATGTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 12 68 Cycle M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 31 32 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 45 GGAGCCTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGATCCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 2 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 14 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GCAATCCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 TC Context M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 GAGTGTTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 15 AA Context M 4.7712 15.0000 2 0 -exampleBAM.bam.bam 45 GGGTTAGG Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 TATATCAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 17 62 Cycle M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 23 TT Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 45 CATGATTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 32 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 44 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ATCCAGTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGTTCTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAATCCAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGATTCTA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCGTCCAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 GT Context M 4.7712 24.0000 2 0 -exampleBAM.bam.bam 24 13 Cycle M 6.0206 1.7696 3 0 -exampleBAM.bam.bam 30 34 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 29 AC Context M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 29 7 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 32 49 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 25 74 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 27 40 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 28 39 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 TTGCAATC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 TT Context M 6.9897 6.0162 4 0 -exampleBAM.bam.bam 30 69 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 71 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 75 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGCAAAAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 19 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 32 TC Context M 6.0206 1.7623 3 0 -exampleBAM.bam.bam 29 37 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 27 CA Context M 4.7712 27.0000 2 0 -exampleBAM.bam.bam 45 ATAAAGAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACTGATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGCCTCG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCACTTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 25 14 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 34 23 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 6 52 Cycle M -0.0000 1.2563 1 1 -exampleBAM.bam.bam 45 TGATATAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTTATCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTATATCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCACTGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGGCCTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 3 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 15 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 17 63 Cycle M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 23 TG Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 45 TTTGTATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 GG Context M 4.7712 24.0000 2 0 -exampleBAM.bam.bam 30 35 Cycle M 4.7712 30.0000 2 0 -exampleBAM.bam.bam 45 TATCATGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGACATGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGATCCAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 33 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 45 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GGAGATTA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATGGTATT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATCTCCAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CGGGTTCG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGGTTAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGGTTCG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 68 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 72 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGTCAATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 18 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 33 TA Context M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TGGGTTAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGGTTCG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTTCTGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 4 TT Context M -0.0000 2.2048 1 1 -exampleBAM.bam.bam 29 4 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 25 73 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 45 AGCCTTTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACTCTTTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 18 58 Cycle M -0.0000 0.0694 1 1 -exampleBAM.bam.bam 45 ATTATTGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACATGATC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 AA Context M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 33 48 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 GTTAGGGT Context D 6.0206 1.7610 3 0 -exampleBAM.bam.bam 32 16 Cycle M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 32 TG Context M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 45 GGCCTGAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 12 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGATTAGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCAGCCTC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATCCATT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTTATAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CATGGTGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 TT Context M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 24 45 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 25 GT Context M 6.0206 1.7678 3 0 -exampleBAM.bam.bam 31 34 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 34 20 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 45 34 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 46 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 ATGAGTCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 51 Cycle M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 TTTTTCTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGGTTGGG Context I 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 GGTTTGGG Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 45 TTAGATTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 30 32 Cycle M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 23 19 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 23 TC Context M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 25 47 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 10 75 Cycle M 3.0103 0.4576 1 0 -exampleBAM.bam.bam 11 GG Context M 3.0103 0.3594 1 0 -exampleBAM.bam.bam 33 TC Context M 8.4510 4.7690 6 0 -exampleBAM.bam.bam 45 TGATCGTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CAGGTTAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCAGTTCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 69 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 73 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 32 51 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 29 AT Context M 4.7712 29.0000 2 0 -exampleBAM.bam.bam 29 5 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 33 49 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 TATTGATA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCATGATA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 32 TT Context M 4.7712 32.0000 2 0 -exampleBAM.bam.bam 45 TGGGGGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTAGGGTT Context D 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 TTCGGGTT Context D 6.0206 1.7610 3 0 -exampleBAM.bam.bam 45 TTGGGGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTGGGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTGGGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTATCAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CGTCCATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCACCATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AAGACACA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 1 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 13 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CTGGGGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 22 TG Context M 6.0206 1.7746 3 0 -exampleBAM.bam.bam 25 GG Context M 4.7712 25.0000 2 0 -exampleBAM.bam.bam 8 CA Context M 3.0103 0.7494 1 0 -exampleBAM.bam.bam 34 21 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 24 GA Context M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 GTGTTGGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCACATGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTCCATGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CACCATGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 35 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 47 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CTATTCTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AATCTAAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 25 46 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 27 76 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 34 55 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 31 1 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 23 18 Cycle M 3.0103 0.0218 1 0 -exampleBAM.bam.bam 31 66 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 45 GAGATTAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCAGGCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 13 AA Context M 3.0103 0.2233 1 0 -exampleBAM.bam.bam 45 GGTTAATG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGTGGAGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 21 TT Context M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 21 17 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 12 AG Context M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 45 GGCCACCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCTGGGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTGGCTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 66 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 26 GT Context M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 TAATCTCC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTGGGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 34 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 45 TTGGGGGT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 17 58 Cycle M 3.0103 0.0875 1 0 -exampleBAM.bam.bam 31 6 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 45 CCTTTGCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 36 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 40 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CAGGCACC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTCTAGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TATTTGCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 TA Context M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 25 CC Context M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 22 23 Cycle M 3.0103 0.0275 1 0 -exampleBAM.bam.bam 45 GAACTGGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 6 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 10 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GGGCTGGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGATATA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTCTTAAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 27 GA Context M 4.7712 27.0000 2 0 -exampleBAM.bam.bam 27 14 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 32 23 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 21 50 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TAACCTGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TCTATTCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 11 40 Cycle M -0.0000 0.3594 1 1 -exampleBAM.bam.bam 45 TTTATTAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATGATTCT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CCTGGAGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GCCAGGCA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 12 AT Context M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 32 53 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 21 TG Context M 6.0206 1.7782 3 0 -exampleBAM.bam.bam 26 GG Context M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 TCTGTGTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTTGGGGG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGGCTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AAATCTAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 67 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CTGGAGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGATTTTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGCACCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTGAAAGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 8 46 Cycle M 3.0103 0.7494 1 0 -exampleBAM.bam.bam 45 TCCAGGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGAGTGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 CG Context M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 45 TTATCATG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ACAGCAAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 37 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 41 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGTGCAAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 TC Context M 6.0206 1.7618 3 0 -exampleBAM.bam.bam 25 CA Context M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 30 AT Context M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 TTTATATC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTACTCTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTATTACT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGTTAAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 7 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 11 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 CCTGAAAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 CTTTGCAC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GTGAACTG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTGGCTTT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 28 2 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 19 30 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 27 GT Context M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 45 64 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 76 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 AGTGTTGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGGGTTGG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GATTCTAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGACACAG Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GGGGTTGG Context I 4.7712 45.0000 2 0 -exampleBAM.bam.bam 15 68 Cycle M 3.0103 0.1396 1 0 -exampleBAM.bam.bam 45 TATAAAGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 22 Cycle M 4.7712 33.0000 2 0 -exampleBAM.bam.bam 12 AA Context M 3.0103 0.2830 1 0 -exampleBAM.bam.bam 32 54 Cycle M 3.0103 0.0027 1 0 -exampleBAM.bam.bam 45 CTCGTCCA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 38 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 42 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 TTAAGTGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTGCAAT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTGCACT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 24 CC Context M 4.7712 24.0000 2 0 -exampleBAM.bam.bam 45 TGAGTCAA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 6 TT Context M 1.7609 6.0000 2 1 -exampleBAM.bam.bam 31 4 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 31 AG Context M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 34 50 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 27 73 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 45 GACACAGC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AACCTGGA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 4 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 8 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 16 58 Cycle M 3.0103 0.1105 1 0 -exampleBAM.bam.bam 30 AA Context M 4.7712 30.0000 2 0 -exampleBAM.bam.bam 24 41 Cycle M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 34 TG Context M 6.0206 1.7618 3 0 -exampleBAM.bam.bam 29 68 Cycle M 3.0103 0.0055 1 0 -exampleBAM.bam.bam 25 9 Cycle M 3.0103 0.0138 1 0 -exampleBAM.bam.bam 26 44 Cycle M 3.0103 0.0109 1 0 -exampleBAM.bam.bam 45 GGTATTAC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGTGAACT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TGGCCTGA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 5 22 Cycle M 3.0103 1.6509 1 0 -exampleBAM.bam.bam 45 AAGTGCAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATTTGCAA Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATCTAATC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 27 GG Context M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 21 48 Cycle M 3.0103 0.0346 1 0 -exampleBAM.bam.bam 45 TGAGTGTT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 13 39 Cycle M 3.0103 0.2233 1 0 -exampleBAM.bam.bam 45 TAAAGACA Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 33 23 Cycle M 3.0103 0.0022 1 0 -exampleBAM.bam.bam 45 GTGGAGCC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 TTTCACAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 65 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GATTTTTC Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 AGTTCTAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 19 61 Cycle M 3.0103 0.0550 1 0 -exampleBAM.bam.bam 28 71 Cycle M 3.0103 0.0069 1 0 -exampleBAM.bam.bam 15 35 Cycle M 3.0103 0.1396 1 0 -exampleBAM.bam.bam 24 CA Context M 3.0103 0.0173 1 0 -exampleBAM.bam.bam 24 10 Cycle M -0.0000 0.0173 1 1 -exampleBAM.bam.bam 45 TTATTGAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATAACCTG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 GAAAGTGC Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 39 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 43 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 31 AT Context M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 31 5 Cycle M 3.0103 0.0035 1 0 -exampleBAM.bam.bam 34 51 Cycle M 3.0103 0.0017 1 0 -exampleBAM.bam.bam 27 72 Cycle M 3.0103 0.0087 1 0 -exampleBAM.bam.bam 30 AC Context M 3.0103 0.0043 1 0 -exampleBAM.bam.bam 45 CATGGTAT Context D 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 ATGATCGT Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 45 5 Cycle D 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 9 Cycle I 7.7815 2.2185 5 0 -exampleBAM.bam.bam 45 GCACCCAG Context I 3.0103 0.0001 1 0 -exampleBAM.bam.bam 34 TT Context M 8.4510 4.7695 6 0 -exampleBAM.bam.bam 31 39 Cycle M 4.7712 31.0000 2 0 -exampleBAM.bam.bam 14 33 Cycle M 3.0103 0.1764 1 0 +ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors +exampleBAM.bam.bam 45 TGAAAGTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGGTATTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGCCTCGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTGTGTCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTGTAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTTAAGTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTATTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 23 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 27 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 ATTCTATT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTAATCTC Context I 3.0103 1 0 +exampleBAM.bam.bam 34 GC Context M 4.7712 2 0 +exampleBAM.bam.bam 8 TG Context M 6.0206 3 0 +exampleBAM.bam.bam 45 TAGAGTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 9 TA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTCGGG Context I 6.0206 3 0 +exampleBAM.bam.bam 45 AGTTTCAC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CATTTCAC Context I 3.0103 1 0 +exampleBAM.bam.bam 16 7 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 5 76 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CATGATAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 53 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 57 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 25 52 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGGCAGCC Context D 3.0103 1 0 +exampleBAM.bam.bam 33 CT Context M 8.4510 6 0 +exampleBAM.bam.bam 45 AAGTGACA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGTGACAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGAGTTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTCTTTGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCCTGAAA Context D 3.0103 1 0 +exampleBAM.bam.bam 12 25 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 75 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 41 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 21 GG Context M 4.7712 2 0 +exampleBAM.bam.bam 26 50 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ACCTGGAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CACAGCAA Context D 3.0103 1 0 +exampleBAM.bam.bam 20 GA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 AGGTGGAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCAAAATC Context I 3.0103 1 0 +exampleBAM.bam.bam 27 TA Context M 6.9897 4 0 +exampleBAM.bam.bam 27 18 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 AAAATCTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 22 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 26 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 33 76 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 30 24 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTATTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTCAATGT Context I 3.0103 1 0 +exampleBAM.bam.bam 21 73 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 17 4 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 8 17 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 GA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 ATCGTGAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CCAGATCC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GATCGTGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 52 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 56 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 9 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 23 CT Context M 4.7712 2 0 +exampleBAM.bam.bam 31 26 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 45 ATGTGAAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATTACTCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ACACAGCA Context D 3.0103 1 0 +exampleBAM.bam.bam 26 TT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GGGTTTGG Context D 4.7712 2 0 +exampleBAM.bam.bam 33 8 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 GT Context M 4.7712 2 0 +exampleBAM.bam.bam 34 74 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATTCTTAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GAGCCTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 20 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTAGGG Context D 4.7712 2 0 +exampleBAM.bam.bam 33 42 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTGCAAAG Context I 3.0103 1 0 +exampleBAM.bam.bam 6 75 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 32 CA Context M 4.7712 2 0 +exampleBAM.bam.bam 29 60 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 13 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 GT Context M 4.7712 2 0 +exampleBAM.bam.bam 21 74 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTAATGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TATTATTG Context D 3.0103 1 0 +exampleBAM.bam.bam 24 52 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTCAGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GACATGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATCATGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 21 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 25 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 34 47 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 25 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 71 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 6 GG Context M 3.9794 4 1 +exampleBAM.bam.bam 9 16 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCCAGTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTCACATG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TAAGTGAC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTGACATG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 55 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 59 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 CATGATCG Context I 3.0103 1 0 +exampleBAM.bam.bam 16 AT Context M 3.0103 1 0 +exampleBAM.bam.bam 32 43 Cycle M 6.0206 3 0 +exampleBAM.bam.bam 19 33 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 GA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 GTATTTGC Context D 3.0103 1 0 +exampleBAM.bam.bam 26 TA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TCTTAAGT Context D 3.0103 1 0 +exampleBAM.bam.bam 33 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 11 20 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 28 61 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 18 1 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ACCCAGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AAAGACAC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCCTTTGC Context D 3.0103 1 0 +exampleBAM.bam.bam 27 16 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 TG Context M 4.7712 2 0 +exampleBAM.bam.bam 32 CT Context M 3.0103 1 0 +exampleBAM.bam.bam 21 44 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATTACTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGGCTGG Context I 3.0103 1 0 +exampleBAM.bam.bam 16 65 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 GG Context M 4.7712 2 0 +exampleBAM.bam.bam 25 21 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 22 9 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CAGGCCAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 20 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 24 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 30 26 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTGTATTT Context D 3.0103 1 0 +exampleBAM.bam.bam 24 53 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 19 70 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 25 55 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AGGCCACC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 54 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 58 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 ACTTTCAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AAAGTGCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATTGATAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AATGTGAA Context I 3.0103 1 0 +exampleBAM.bam.bam 9 TT Context M 3.0103 1 0 +exampleBAM.bam.bam 19 32 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 28 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CGGGTTTG Context I 4.7712 2 0 +exampleBAM.bam.bam 45 TCTTTGTA Context I 3.0103 1 0 +exampleBAM.bam.bam 33 10 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 CA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 GTTCGGGT Context I 6.0206 3 0 +exampleBAM.bam.bam 27 TT Context M 4.7712 2 0 +exampleBAM.bam.bam 27 17 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CAGCAAAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GGCAGCCT Context I 3.0103 1 0 +exampleBAM.bam.bam 20 GT Context M -0.0000 1 1 +exampleBAM.bam.bam 45 TGGAGCCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGTGGCC Context I 3.0103 1 0 +exampleBAM.bam.bam 28 30 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 40 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 24 TG Context M 4.7712 2 0 +exampleBAM.bam.bam 45 TGTGTCTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCAATAAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCTCCAGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 49 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 61 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 CCTCGTCC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGCACCCA Context I 3.0103 1 0 +exampleBAM.bam.bam 22 44 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 45 AGGTTATC Context I 3.0103 1 0 +exampleBAM.bam.bam 34 41 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 65 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 12 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 GG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTGTGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGTTGGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 24 50 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTTCACA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCGGGTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TAGGGTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 33 73 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 9 52 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 19 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 31 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 25 TA Context M 6.0206 3 0 +exampleBAM.bam.bam 34 11 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 28 25 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TAGATTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTGGGG Context I 4.7712 2 0 +exampleBAM.bam.bam 45 GGCTGGGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GATTAGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 5 GG Context M 3.0103 3 1 +exampleBAM.bam.bam 32 15 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 22 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 42 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 5 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 AT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTCAGGC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGCCAGGC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTCTTTAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGAACTGG Context I 3.0103 1 0 +exampleBAM.bam.bam 26 20 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATTCTTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGATAACC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATTTTTCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGCTTTAT Context I 3.0103 1 0 +exampleBAM.bam.bam 5 46 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 29 27 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATCCATTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 48 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 60 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GATCCAGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AATGAGTC Context D 3.0103 1 0 +exampleBAM.bam.bam 24 TT Context M 3.0103 3 1 +exampleBAM.bam.bam 45 TCTTTATA Context I 3.0103 1 0 +exampleBAM.bam.bam 6 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 23 GT Context M 4.7712 2 0 +exampleBAM.bam.bam 34 40 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 18 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 30 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 CAAAATCT Context I 3.0103 1 0 +exampleBAM.bam.bam 22 15 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CCAGGTTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCATGGTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCTAATCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGTTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TAGGGTTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGTTA Context I 3.0103 1 0 +exampleBAM.bam.bam 33 72 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 60 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 CA Context M 6.9897 4 0 +exampleBAM.bam.bam 45 CCCAGATC Context D 3.0103 1 0 +exampleBAM.bam.bam 18 36 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 16 70 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGTATTTG Context I 3.0103 1 0 +exampleBAM.bam.bam 33 46 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTGGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTTTGGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTAGAG Context I 3.0103 1 0 +exampleBAM.bam.bam 19 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 32 GA Context M 4.7712 2 0 +exampleBAM.bam.bam 32 14 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 12 62 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 12 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTGGCCT Context I 3.0103 1 0 +exampleBAM.bam.bam 4 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 27 53 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 23 GA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTATTATT Context I 3.0103 1 0 +exampleBAM.bam.bam 5 74 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATGATAAC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 51 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 63 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 CACCCAGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CGTGAGTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCTTTATT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATGGTGGC Context D 3.0103 1 0 +exampleBAM.bam.bam 34 CT Context M 4.7712 2 0 +exampleBAM.bam.bam 4 72 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCGGGTTT Context I 4.7712 2 0 +exampleBAM.bam.bam 24 48 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCCATGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CACATGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 17 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 29 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 ATCAATAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ACCATGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 32 GT Context M 8.4510 6 0 +exampleBAM.bam.bam 19 7 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 45 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 28 27 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCCATTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GATAACCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AACTGGGA Context I 3.0103 1 0 +exampleBAM.bam.bam 4 GG Context M 3.0103 1 0 +exampleBAM.bam.bam 33 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TCAGGCCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGCACTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTCACTGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTCCAGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 6 CT Context M 3.0103 1 0 +exampleBAM.bam.bam 23 15 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 51 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 72 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 42 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GATATAAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTAGAGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 50 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 62 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GCCACCAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGGTTCGG Context D 6.0206 3 0 +exampleBAM.bam.bam 24 TC Context M 6.0206 3 0 +exampleBAM.bam.bam 25 TT Context M 4.7712 2 0 +exampleBAM.bam.bam 45 16 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 28 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 ACATGGTA Context I 3.0103 1 0 +exampleBAM.bam.bam 16 34 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 45 AATCTCCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATTTCACT Context I 3.0103 1 0 +exampleBAM.bam.bam 22 GT Context M 4.7712 2 0 +exampleBAM.bam.bam 45 ATATCAAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAATGTGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GAGTCAAT Context D 3.0103 1 0 +exampleBAM.bam.bam 24 49 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGGGGTTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TAGGGTTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGCAATCC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGGGTTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTAATGAG Context I 3.0103 1 0 +exampleBAM.bam.bam 30 30 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 75 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 GG Context M 7.7815 5 0 +exampleBAM.bam.bam 20 9 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 20 CT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 ATTAGATT Context D 3.0103 1 0 +exampleBAM.bam.bam 33 44 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTCTGTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGAGATT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTTGGGC Context I 3.0103 1 0 +exampleBAM.bam.bam 21 11 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 24 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 46 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 55 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATATAAAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GAGTTTCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CACTTTCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CCATTTCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CCAGGCAC Context D 3.0103 1 0 +exampleBAM.bam.bam 11 TT Context M -0.0000 1 1 +exampleBAM.bam.bam 45 TTTCACTG Context I 3.0103 1 0 +exampleBAM.bam.bam 33 GA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TCGTGAGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TACTCTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TAATGAGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTGTCTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGCTTTAT Context D 3.0103 1 0 +exampleBAM.bam.bam 22 70 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATTTTTCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGCCAGGC Context I 3.0103 1 0 +exampleBAM.bam.bam 33 1 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 45 TTTCAGGC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TATTCTTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGATAACC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTCTTTAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGAACTGG Context D 3.0103 1 0 +exampleBAM.bam.bam 21 AG Context M 4.7712 2 0 +exampleBAM.bam.bam 32 33 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 27 56 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGCTGGGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GATTAGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 33 35 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TAGATTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTGGGG Context D 4.7712 2 0 +exampleBAM.bam.bam 19 CT Context M 1.7609 2 1 +exampleBAM.bam.bam 45 19 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 31 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 TGTTGGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTGTGT Context I 3.0103 1 0 +exampleBAM.bam.bam 24 62 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCGGGTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTTCACA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TAGGGTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 30 TT Context M 4.7712 2 0 +exampleBAM.bam.bam 30 17 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 33 69 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 6 36 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 17 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 21 64 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 16 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CCTCGTCC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 49 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 61 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 AGGTTATC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGCACCCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGTGTCTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCAATAAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCTCCAGG Context D 3.0103 1 0 +exampleBAM.bam.bam 6 AA Context M 4.7712 2 0 +exampleBAM.bam.bam 31 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 31 19 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 8 58 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 28 54 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTGGCCT Context D 3.0103 1 0 +exampleBAM.bam.bam 18 10 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 18 CA Context M 4.7712 2 0 +exampleBAM.bam.bam 27 57 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 AT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TGTATTTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTAGAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTGGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTTGGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 13 TA Context M 3.0103 1 0 +exampleBAM.bam.bam 20 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CCCAGATC Context I 3.0103 1 0 +exampleBAM.bam.bam 32 2 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 27 27 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 6 67 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TAGGGTTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGTTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCATGGTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCTAATCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGTTA Context D 3.0103 1 0 +exampleBAM.bam.bam 30 TG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 18 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 30 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CCAGGTTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAAAATCT Context D 3.0103 1 0 +exampleBAM.bam.bam 25 31 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 6 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 17 GG Context M 3.0103 1 0 +exampleBAM.bam.bam 23 35 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCTTTATA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GATCCAGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 48 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 60 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 ATCCATTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AATGAGTC Context I 3.0103 1 0 +exampleBAM.bam.bam 31 TA Context M 4.7712 2 0 +exampleBAM.bam.bam 21 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 34 65 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CTCCAGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 18 CT Context M 3.0103 1 0 +exampleBAM.bam.bam 33 3 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCAGGCCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTGCACTT Context D 3.0103 1 0 +exampleBAM.bam.bam 28 53 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTCACTGA Context D 3.0103 1 0 +exampleBAM.bam.bam 19 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 32 1 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GATAACCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AACTGGGA Context D 3.0103 1 0 +exampleBAM.bam.bam 16 73 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCCATTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 21 66 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 5 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 AT Context M 8.4510 6 0 +exampleBAM.bam.bam 16 47 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CACATGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 17 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 29 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 ATCAATAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ACCATGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCGGGTTT Context D 4.7712 2 0 +exampleBAM.bam.bam 45 TCCATGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 6 AG Context M -0.0000 1 1 +exampleBAM.bam.bam 6 4 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 TT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 ATGATAAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 51 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 63 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CGTGAGTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CACCCAGA Context D 3.0103 1 0 +exampleBAM.bam.bam 16 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 5 70 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GCTTTATT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATGGTGGC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTATTATT Context D 3.0103 1 0 +exampleBAM.bam.bam 34 64 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 AC Context M 6.0206 3 0 +exampleBAM.bam.bam 33 2 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTCACTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCGTGAGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTGTCTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TAATGAGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TACTCTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CACTTTCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CCATTTCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATATAAAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GAGTTTCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CCAGGCAC Context I 3.0103 1 0 +exampleBAM.bam.bam 29 54 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 6 65 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 10 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 CA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 TTTCTGTG Context D 3.0103 1 0 +exampleBAM.bam.bam 33 32 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTTGGGC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGGAGATT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATTAGATT Context I 3.0103 1 0 +exampleBAM.bam.bam 34 4 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 67 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGGGGTTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGCAATCC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGGGGTTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TAGGGTTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTAATGAG Context D 3.0103 1 0 +exampleBAM.bam.bam 30 18 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 30 TA Context M 6.9897 4 0 +exampleBAM.bam.bam 45 16 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 28 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 ACATGGTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GAGTCAAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CAATGTGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AATCTCCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATTTCACT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATATCAAT Context I 3.0103 1 0 +exampleBAM.bam.bam 8 57 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 34 38 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 16 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 TG Context M 6.0206 3 0 +exampleBAM.bam.bam 45 GGGTTCGG Context I 6.0206 3 0 +exampleBAM.bam.bam 45 CTAGAGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 50 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 62 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 GATATAAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCCACCAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ACCTGGAG Context I 3.0103 1 0 +exampleBAM.bam.bam 5 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 AGGTGGAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCAAAATC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CACAGCAA Context I 3.0103 1 0 +exampleBAM.bam.bam 28 TT Context M 3.0103 1 0 +exampleBAM.bam.bam 33 39 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 23 64 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 27 30 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 AAGTGACA Context D 3.0103 1 0 +exampleBAM.bam.bam 5 38 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AGAGTTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGTGACAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCCTGAAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTCTTTGT Context I 3.0103 1 0 +exampleBAM.bam.bam 33 AT Context M 4.7712 2 0 +exampleBAM.bam.bam 45 TGGCAGCC Context I 3.0103 1 0 +exampleBAM.bam.bam 4 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 29 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 34 71 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AGTTTCAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CATTTCAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 53 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 57 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CATGATAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TAGAGTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTCGGG Context D 6.0206 3 0 +exampleBAM.bam.bam 45 CTTTATTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTGTAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGCCTCGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTGTGTCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTTAAGTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATTCTATT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTAATCTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 23 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 27 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 30 21 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGAAAGTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGTATTA Context I 3.0103 1 0 +exampleBAM.bam.bam 23 38 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 3 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTAGGG Context I 4.7712 2 0 +exampleBAM.bam.bam 45 GTGCAAAG Context D 3.0103 1 0 +exampleBAM.bam.bam 28 TG Context M 6.0206 3 0 +exampleBAM.bam.bam 45 ATTCTTAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GAGCCTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 27 31 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 48 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 19 GG Context M 4.7712 2 0 +exampleBAM.bam.bam 4 37 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGGTTTGG Context I 4.7712 2 0 +exampleBAM.bam.bam 33 AG Context M 6.0206 3 0 +exampleBAM.bam.bam 28 50 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATTACTCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ACACAGCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATGTGAAC Context I 3.0103 1 0 +exampleBAM.bam.bam 32 36 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 29 TA Context M 4.7712 2 0 +exampleBAM.bam.bam 34 70 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 17 76 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 30 54 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 24 25 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATCGTGAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GATCGTGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 52 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 56 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CCAGATCC Context D 3.0103 1 0 +exampleBAM.bam.bam 16 CA Context M 3.0103 1 0 +exampleBAM.bam.bam 8 63 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 14 TG Context M 3.0103 1 0 +exampleBAM.bam.bam 23 AT Context M 6.0206 3 0 +exampleBAM.bam.bam 19 72 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 30 20 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTATTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTCAATGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AAAATCTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 22 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 26 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 34 2 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 6 68 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 23 66 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 28 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 AT Context M 4.7712 2 0 +exampleBAM.bam.bam 5 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TATTACTC Context D 3.0103 1 0 +exampleBAM.bam.bam 33 37 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGGGCTGG Context D 3.0103 1 0 +exampleBAM.bam.bam 28 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 4 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 29 TT Context M 4.7712 2 0 +exampleBAM.bam.bam 18 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 AAAGACAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCCTTTGC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ACCCAGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCTTAAGT Context I 3.0103 1 0 +exampleBAM.bam.bam 13 55 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTATTTGC Context I 3.0103 1 0 +exampleBAM.bam.bam 33 7 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 23 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 8 60 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 22 38 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CATGATCG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 55 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 59 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 TCCAGTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTGACATG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTCACATG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TAAGTGAC Context D 3.0103 1 0 +exampleBAM.bam.bam 4 64 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 25 24 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 22 AG Context M 4.7712 2 0 +exampleBAM.bam.bam 45 CTTTCAGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATCATGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 21 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 25 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 GACATGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 30 23 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 67 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 24 56 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATTATTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTTAATGA Context D 3.0103 1 0 +exampleBAM.bam.bam 32 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 23 67 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGGAGCCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGGTGGCC Context D 3.0103 1 0 +exampleBAM.bam.bam 28 TA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CAGCAAAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGCAGCCT Context D 3.0103 1 0 +exampleBAM.bam.bam 34 68 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 3 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCTTTGTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTCGGGT Context D 6.0206 3 0 +exampleBAM.bam.bam 28 48 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 18 GG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CGGGTTTG Context D 4.7712 2 0 +exampleBAM.bam.bam 34 34 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 30 52 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 24 27 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AGGCCACC Context D 3.0103 1 0 +exampleBAM.bam.bam 20 69 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AAAGTGCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATTGATAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AATGTGAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 54 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 58 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 ACTTTCAG Context D 3.0103 1 0 +exampleBAM.bam.bam 23 37 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 71 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 66 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 15 TG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTGTATTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 20 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 24 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CAGGCCAC Context I 3.0103 1 0 +exampleBAM.bam.bam 23 59 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 17 20 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 30 CG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTGATATA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTTAAG Context I 3.0103 1 0 +exampleBAM.bam.bam 15 14 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GAACTGGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 6 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 10 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GGGCTGGG Context D 3.0103 1 0 +exampleBAM.bam.bam 31 10 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 60 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 37 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 6 31 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 30 42 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTCTAGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TATTTGCA Context D 3.0103 1 0 +exampleBAM.bam.bam 24 5 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CCTTTGCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAGGCACC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 36 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 40 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 29 GA Context M 4.7712 2 0 +exampleBAM.bam.bam 21 29 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TAATCTCC Context I 3.0103 1 0 +exampleBAM.bam.bam 15 74 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 33 24 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCTGGGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 66 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CTTGGCTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGCCACCA Context D 3.0103 1 0 +exampleBAM.bam.bam 19 TG Context M 4.7712 2 0 +exampleBAM.bam.bam 45 TTCAGGCC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTAATG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GGTGGAGC Context I 3.0103 1 0 +exampleBAM.bam.bam 28 GG Context M 6.0206 3 0 +exampleBAM.bam.bam 45 GAGATTAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 7 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 11 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 TTACTCTT Context I 3.0103 1 0 +exampleBAM.bam.bam 30 9 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTATATC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGTTAAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTATTACT Context D 3.0103 1 0 +exampleBAM.bam.bam 31 11 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 34 61 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 36 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ACAGCAAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGTGCAAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 37 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 41 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 TCCAGGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTGAGTGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTATCATG Context D 3.0103 1 0 +exampleBAM.bam.bam 24 AG Context M 4.7712 2 0 +exampleBAM.bam.bam 29 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 32 57 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 67 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 18 19 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CTGGAGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGATTTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AAATCTAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTGAAAGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGGCACCC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCTGTGTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGCTG Context D 3.0103 1 0 +exampleBAM.bam.bam 28 47 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGGGG Context I 3.0103 1 0 +exampleBAM.bam.bam 19 TT Context M 4.7712 2 0 +exampleBAM.bam.bam 29 45 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CCTGGAGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATGATTCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCCAGGCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTATTAT Context I 3.0103 1 0 +exampleBAM.bam.bam 33 59 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCTATTCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TAACCTGG Context I 3.0103 1 0 +exampleBAM.bam.bam 30 CA Context M 6.0206 3 0 +exampleBAM.bam.bam 15 GG Context M 4.7712 2 0 +exampleBAM.bam.bam 45 GACACAGC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AACCTGGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 4 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 8 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 25 AT Context M 4.7712 2 0 +exampleBAM.bam.bam 6 63 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 45 TTTGCAAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGCACT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTAAGTGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGAGTCAA Context I 3.0103 1 0 +exampleBAM.bam.bam 22 59 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CTCGTCCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 38 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 42 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 34 62 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 CG Context M 3.0103 1 0 +exampleBAM.bam.bam 31 8 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 27 69 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 26 3 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATAAAGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGGGTTGG Context D 4.7712 2 0 +exampleBAM.bam.bam 45 64 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 76 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GATTCTAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGACACAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGGGTTGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGTGTTGG Context D 3.0103 1 0 +exampleBAM.bam.bam 29 12 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 GG Context M 6.9897 4 0 +exampleBAM.bam.bam 8 71 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTGAACTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGCTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 9 69 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CCTGAAAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTGCAC Context D 3.0103 1 0 +exampleBAM.bam.bam 20 29 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 12 40 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 24 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 61 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CATGGTAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCACCCAG Context D 3.0103 1 0 +exampleBAM.bam.bam 16 55 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATGATCGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 5 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 9 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 30 CC Context M 4.7712 2 0 +exampleBAM.bam.bam 23 56 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 6 62 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 43 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 ATAACCTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 39 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 43 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GAAAGTGC Context D 3.0103 1 0 +exampleBAM.bam.bam 24 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 24 6 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 45 TTATTGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 34 63 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 CT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 65 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 18 TT Context M -0.0000 1 1 +exampleBAM.bam.bam 45 GATTTTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGTTCTAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TAAAGACA Context I 3.0103 1 0 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+exampleBAM.bam.bam 45 ATCCAGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 32 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 44 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 CATGATTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAATCCAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAGTTCTA Context I 3.0103 1 0 +exampleBAM.bam.bam 34 26 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 8 AT Context M -0.0000 1 1 +exampleBAM.bam.bam 45 GGGTTAGG Context D 4.7712 2 0 +exampleBAM.bam.bam 30 12 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATATCAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCAATCCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGAGCCTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAGATCCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 2 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 14 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GAGTGTTG Context I 3.0103 1 0 +exampleBAM.bam.bam 32 30 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 21 59 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGTCTTTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCAATGTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGCTTTA Context I 3.0103 1 0 +exampleBAM.bam.bam 13 GA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CCATGATT Context D 3.0103 1 0 +exampleBAM.bam.bam 29 CA Context M 3.0103 1 0 +exampleBAM.bam.bam 19 54 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATCAATA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGGGCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGTTAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGCACTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCTAGAGT Context I 3.0103 1 0 +exampleBAM.bam.bam 26 AT Context M 3.0103 1 0 +exampleBAM.bam.bam 20 57 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GCCTCGTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 70 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 74 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 18 22 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 32 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 66 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 15 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 31 GC Context M 6.0206 3 0 +exampleBAM.bam.bam 45 33 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 45 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GGAGATTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGATCCAG Context D 3.0103 1 0 +exampleBAM.bam.bam 16 19 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 ATGGTATT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATCTCCAG Context D 3.0103 1 0 +exampleBAM.bam.bam 13 75 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGTATT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TATCATGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGACATGG Context I 3.0103 1 0 +exampleBAM.bam.bam 17 TT Context M 3.0103 3 1 +exampleBAM.bam.bam 31 45 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 8 AG Context M 4.7712 2 0 +exampleBAM.bam.bam 34 27 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 3 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 15 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 TTATATCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGATATAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTATCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCACTGAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTGGCCTG Context D 3.0103 1 0 +exampleBAM.bam.bam 19 21 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 32 31 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CACTGATG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATAAAGAC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCACTTTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CAGCCTCG Context I 3.0103 1 0 +exampleBAM.bam.bam 28 CT Context M 4.7712 2 0 +exampleBAM.bam.bam 45 71 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 75 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 AGCAAAAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGCAATC Context I 3.0103 1 0 +exampleBAM.bam.bam 33 29 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 26 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTTGGG Context D 4.7712 2 0 +exampleBAM.bam.bam 45 GGGTTGGG Context D 6.0206 3 0 +exampleBAM.bam.bam 24 3 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTTTCTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTAGATTT Context D 3.0103 1 0 +exampleBAM.bam.bam 16 TG Context M 4.7712 2 0 +exampleBAM.bam.bam 45 34 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 46 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 ATGAGTCA Context D 3.0103 1 0 +exampleBAM.bam.bam 27 65 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 12 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 GG Context M 6.9897 4 0 +exampleBAM.bam.bam 34 58 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 24 33 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 15 8 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 26 67 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 30 GA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 12 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GGCCTGAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGATTAGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCAGCCTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CATGGTGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AATCCATT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTATAT Context D 3.0103 1 0 +exampleBAM.bam.bam 29 76 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 61 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 28 CA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 GTTAGGGT Context I 6.0206 3 0 +exampleBAM.bam.bam 45 ACTCTTTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGCCTTTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ACATGATC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATTATTGA Context D 3.0103 1 0 +exampleBAM.bam.bam 32 28 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 29 42 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 AT Context M 6.9897 4 0 +exampleBAM.bam.bam 45 TGGGTTAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGGTTCG Context D 3.0103 1 0 +exampleBAM.bam.bam 26 7 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTTCTGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGGGTTAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGGGTTCG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CGGGTTCG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 68 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 72 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 AGTCAATG Context I 3.0103 1 0 +exampleBAM.bam.bam 29 8 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 CG Context M 4.7712 2 0 +exampleBAM.bam.bam 4 29 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 16 TT Context M 3.9794 4 1 +exampleBAM.bam.bam 45 CACCATGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 35 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 47 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 CTATTCTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AATCTAAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTGTTGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 30 45 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCACATGA Context I 3.0103 1 0 +exampleBAM.bam.bam 9 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GTCCATGA Context I 3.0103 1 0 +exampleBAM.bam.bam 31 13 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 34 59 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AAGACACA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CCACCATG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 1 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 13 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 16 51 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CGTCCATG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTGGGGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTCGGGTT Context I 6.0206 3 0 +exampleBAM.bam.bam 45 TTAGGGTT Context I 6.0206 3 0 +exampleBAM.bam.bam 45 TGGGGGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGGGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 9 38 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTATCAT Context I 3.0103 1 0 +exampleBAM.bam.bam 30 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 17 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 34 25 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CCATGATA Context D 3.0103 1 0 +exampleBAM.bam.bam 28 11 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATTGATA Context D 3.0103 1 0 +exampleBAM.bam.bam 29 43 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CCAGTTCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAGGTTAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 69 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 73 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 28 41 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 31 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGATCGTG Context D 3.0103 1 0 +exampleBAM.bam.bam 29 9 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 12 GC Context M 3.0103 1 0 +exampleBAM.bam.bam 29 6 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GCCTCGTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 70 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 74 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 TTTGGGCT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TATCAATA Context D 3.0103 1 0 +exampleBAM.bam.bam 33 TG Context M 6.0206 3 0 +exampleBAM.bam.bam 45 TTGGTTAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCTAGAGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGCACTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 4 49 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 18 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 10 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 27 11 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CCATGATT Context I 3.0103 1 0 +exampleBAM.bam.bam 5 TT Context M 1.7609 2 1 +exampleBAM.bam.bam 18 56 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGGCTTTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGTCTTTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCAATGTG Context D 3.0103 1 0 +exampleBAM.bam.bam 12 68 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 32 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGAGCCTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CAGATCCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 2 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 14 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 GCAATCCA Context I 3.0103 1 0 +exampleBAM.bam.bam 22 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GAGTGTTG Context D 3.0103 1 0 +exampleBAM.bam.bam 15 AA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 GGGTTAGG Context I 4.7712 2 0 +exampleBAM.bam.bam 45 TATATCAA Context D 3.0103 1 0 +exampleBAM.bam.bam 17 62 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 TT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CATGATTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 32 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 44 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 ATCCAGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CAGTTCTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CAATCCAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGATTCTA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCGTCCAT Context I 3.0103 1 0 +exampleBAM.bam.bam 24 GT Context M 4.7712 2 0 +exampleBAM.bam.bam 24 13 Cycle M 6.0206 3 0 +exampleBAM.bam.bam 30 34 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 29 7 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 49 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 74 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 40 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 28 39 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTGCAATC Context D 3.0103 1 0 +exampleBAM.bam.bam 33 TT Context M 6.9897 4 0 +exampleBAM.bam.bam 30 69 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 71 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 75 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 AGCAAAAT Context D 3.0103 1 0 +exampleBAM.bam.bam 32 19 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 TC Context M 6.0206 3 0 +exampleBAM.bam.bam 29 37 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 CA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 ATAAAGAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CACTGATG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CAGCCTCG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCACTTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 25 14 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 23 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 6 52 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 45 TGATATAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTATCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTATATCA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCACTGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTGGCCTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 3 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 15 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 17 63 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 TG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGTATT Context D 3.0103 1 0 +exampleBAM.bam.bam 24 GG Context M 4.7712 2 0 +exampleBAM.bam.bam 30 35 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 45 TATCATGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGACATGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGATCCAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 33 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 45 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 GGAGATTA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATGGTATT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATCTCCAG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CGGGTTCG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGGGTTAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGGGTTCG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 68 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 72 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 AGTCAATG Context D 3.0103 1 0 +exampleBAM.bam.bam 33 18 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 TA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TGGGTTAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGGGTTCG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTTCTGT Context D 3.0103 1 0 +exampleBAM.bam.bam 4 TT Context M -0.0000 1 1 +exampleBAM.bam.bam 29 4 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 73 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AGCCTTTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ACTCTTTG Context D 3.0103 1 0 +exampleBAM.bam.bam 18 58 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 45 ATTATTGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ACATGATC Context I 3.0103 1 0 +exampleBAM.bam.bam 28 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 33 48 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTTAGGGT Context D 6.0206 3 0 +exampleBAM.bam.bam 32 16 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 32 TG Context M 4.7712 2 0 +exampleBAM.bam.bam 45 GGCCTGAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 12 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 AGATTAGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCAGCCTC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AATCCATT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTATAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CATGGTGG Context I 3.0103 1 0 +exampleBAM.bam.bam 22 TT Context M 3.0103 1 0 +exampleBAM.bam.bam 24 45 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 GT Context M 6.0206 3 0 +exampleBAM.bam.bam 31 34 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 20 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 34 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 46 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 ATGAGTCA Context I 3.0103 1 0 +exampleBAM.bam.bam 22 51 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTTTCTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGGTTGGG Context I 6.0206 3 0 +exampleBAM.bam.bam 45 GGTTTGGG Context I 4.7712 2 0 +exampleBAM.bam.bam 45 TTAGATTT Context I 3.0103 1 0 +exampleBAM.bam.bam 30 32 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 19 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 TC Context M 3.0103 1 0 +exampleBAM.bam.bam 25 47 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 10 75 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 11 GG Context M 3.0103 1 0 +exampleBAM.bam.bam 33 TC Context M 8.4510 6 0 +exampleBAM.bam.bam 45 TGATCGTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CAGGTTAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CCAGTTCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 69 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 73 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 32 51 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 AT Context M 4.7712 2 0 +exampleBAM.bam.bam 29 5 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 33 49 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATTGATA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CCATGATA Context I 3.0103 1 0 +exampleBAM.bam.bam 32 TT Context M 4.7712 2 0 +exampleBAM.bam.bam 45 TGGGGGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTAGGGTT Context D 6.0206 3 0 +exampleBAM.bam.bam 45 TTCGGGTT Context D 6.0206 3 0 +exampleBAM.bam.bam 45 TTGGGGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGGGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTATCAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CGTCCATG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CCACCATG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AAGACACA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 1 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 13 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CTGGGGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 22 TG Context M 6.0206 3 0 +exampleBAM.bam.bam 25 GG Context M 4.7712 2 0 +exampleBAM.bam.bam 8 CA Context M 3.0103 1 0 +exampleBAM.bam.bam 34 21 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 24 GA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GTGTTGGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TCACATGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTCCATGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CACCATGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 35 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 47 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CTATTCTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AATCTAAT Context D 3.0103 1 0 +exampleBAM.bam.bam 25 46 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 76 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 55 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 1 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 23 18 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 66 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GAGATTAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTCAGGCC Context D 3.0103 1 0 +exampleBAM.bam.bam 13 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTTAATG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGTGGAGC Context D 3.0103 1 0 +exampleBAM.bam.bam 21 TT Context M 3.0103 1 0 +exampleBAM.bam.bam 21 17 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 12 AG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 GGCCACCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GCTGGGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTTGGCTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 66 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 26 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TAATCTCC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 28 34 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGGGT Context D 3.0103 1 0 +exampleBAM.bam.bam 17 58 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 6 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CCTTTGCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 36 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 40 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CAGGCACC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTCTAGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TATTTGCA Context I 3.0103 1 0 +exampleBAM.bam.bam 34 TA Context M 3.0103 1 0 +exampleBAM.bam.bam 25 CC Context M 3.0103 1 0 +exampleBAM.bam.bam 22 23 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GAACTGGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 6 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 10 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 GGGCTGGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTGATATA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTCTTAAG Context D 3.0103 1 0 +exampleBAM.bam.bam 27 GA Context M 4.7712 2 0 +exampleBAM.bam.bam 27 14 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 32 23 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 50 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TAACCTGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TCTATTCT Context I 3.0103 1 0 +exampleBAM.bam.bam 11 40 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 45 TTTATTAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATGATTCT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CCTGGAGA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GCCAGGCA Context D 3.0103 1 0 +exampleBAM.bam.bam 12 AT Context M 3.0103 1 0 +exampleBAM.bam.bam 32 53 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 TG Context M 6.0206 3 0 +exampleBAM.bam.bam 26 GG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TCTGTGTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTTGGGGG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGGCTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AAATCTAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 67 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 CTGGAGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGATTTTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGGCACCC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 CTGAAAGT Context I 3.0103 1 0 +exampleBAM.bam.bam 8 46 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TCCAGGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTGAGTGT Context I 3.0103 1 0 +exampleBAM.bam.bam 24 CG Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTATCATG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ACAGCAAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 37 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 41 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 AGTGCAAA Context I 3.0103 1 0 +exampleBAM.bam.bam 34 TC Context M 6.0206 3 0 +exampleBAM.bam.bam 25 CA Context M 3.0103 1 0 +exampleBAM.bam.bam 30 AT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 TTTATATC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTACTCTT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GTATTACT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGTTAAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 7 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 11 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 CCTGAAAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 CTTTGCAC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTGAACTG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TTGGCTTT Context I 3.0103 1 0 +exampleBAM.bam.bam 28 2 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 19 30 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 GT Context M 3.0103 1 0 +exampleBAM.bam.bam 45 64 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 76 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 AGTGTTGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGGGTTGG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GATTCTAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 AGACACAG Context D 3.0103 1 0 +exampleBAM.bam.bam 45 GGGGTTGG Context I 4.7712 2 0 +exampleBAM.bam.bam 15 68 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TATAAAGA Context I 3.0103 1 0 +exampleBAM.bam.bam 33 22 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 12 AA Context M 3.0103 1 0 +exampleBAM.bam.bam 32 54 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 CTCGTCCA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 38 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 42 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 TTAAGTGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGCAAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTGCACT Context D 3.0103 1 0 +exampleBAM.bam.bam 24 CC Context M 4.7712 2 0 +exampleBAM.bam.bam 45 TGAGTCAA Context D 3.0103 1 0 +exampleBAM.bam.bam 6 TT Context M 1.7609 2 1 +exampleBAM.bam.bam 31 4 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 AG Context M 4.7712 2 0 +exampleBAM.bam.bam 34 50 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 73 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GACACAGC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AACCTGGA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 4 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 8 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 16 58 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 30 AA Context M 4.7712 2 0 +exampleBAM.bam.bam 24 41 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 TG Context M 6.0206 3 0 +exampleBAM.bam.bam 29 68 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 25 9 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 26 44 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GGTATTAC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGTGAACT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGGCCTGA Context D 3.0103 1 0 +exampleBAM.bam.bam 5 22 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 AAGTGCAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATTTGCAA Context I 3.0103 1 0 +exampleBAM.bam.bam 45 ATCTAATC Context D 3.0103 1 0 +exampleBAM.bam.bam 27 GG Context M 3.0103 1 0 +exampleBAM.bam.bam 21 48 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TGAGTGTT Context D 3.0103 1 0 +exampleBAM.bam.bam 13 39 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 TAAAGACA Context D 3.0103 1 0 +exampleBAM.bam.bam 33 23 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 45 GTGGAGCC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTCACAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 65 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 GATTTTTC Context D 3.0103 1 0 +exampleBAM.bam.bam 45 AGTTCTAG Context I 3.0103 1 0 +exampleBAM.bam.bam 19 61 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 28 71 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 15 35 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 24 CA Context M 3.0103 1 0 +exampleBAM.bam.bam 24 10 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 45 TTATTGAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATAACCTG Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GAAAGTGC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 39 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 43 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 31 AT Context M 4.7712 2 0 +exampleBAM.bam.bam 31 5 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 51 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 27 72 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 30 AC Context M 3.0103 1 0 +exampleBAM.bam.bam 45 CATGGTAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATGATCGT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 5 Cycle D 7.7815 5 0 +exampleBAM.bam.bam 45 9 Cycle I 7.7815 5 0 +exampleBAM.bam.bam 45 GCACCCAG Context I 3.0103 1 0 +exampleBAM.bam.bam 34 TT Context M 8.4510 6 0 +exampleBAM.bam.bam 31 39 Cycle M 4.7712 2 0 +exampleBAM.bam.bam 14 33 Cycle M 3.0103 1 0