From a19c27297f0b5226849fdfbf1f6c939f617fbfbc Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 5 Apr 2012 10:19:52 -0400 Subject: [PATCH 01/14] continuing the BQSR triage... * fixed the loading of the new reduced size reports * reduced BQSR scala script memory to 2Gb * removed dcov parameter from BQSR scala script * fixed estimatedQReported calculation from -log10(pe) to -10*log10(pe). * updated md5's with the proper PHRED scaled EstimatedQReported --- .../sting/gatk/walkers/bqsr/RecalDatum.java | 14 +- .../walkers/bqsr/RecalibrationReport.java | 15 +- public/testdata/exampleGRP.grp | 2786 ++++++++--------- 3 files changed, 1410 insertions(+), 1405 deletions(-) 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/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 +exampleBAM.bam.bam 45 TGAGTGTT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TTTCACAT Context I 3.0103 1 0 +exampleBAM.bam.bam 45 GTGGAGCC Context D 3.0103 1 0 +exampleBAM.bam.bam 19 49 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 GT Context M 4.7712 2 0 +exampleBAM.bam.bam 5 26 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 45 AAGTGCAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATTTGCAA Context D 3.0103 1 0 +exampleBAM.bam.bam 45 ATCTAATC Context I 3.0103 1 0 +exampleBAM.bam.bam 20 28 Cycle M -0.0000 1 1 +exampleBAM.bam.bam 45 GGTATTAC Context I 3.0103 1 0 +exampleBAM.bam.bam 45 TGTGAACT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGGCCTGA Context I 3.0103 1 0 +exampleBAM.bam.bam 33 57 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 21 60 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 29 47 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 34 56 Cycle M 3.0103 1 0 +exampleBAM.bam.bam 31 GA Context M 4.7712 2 0 +exampleBAM.bam.bam 45 TCGTCCAT Context D 3.0103 1 0 +exampleBAM.bam.bam 45 TGATTCTA Context I 3.0103 1 0 +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 From c77104b81530e972dd152794551d486fbe622a22 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Fri, 6 Apr 2012 00:22:52 -0400 Subject: [PATCH 02/14] Adding function call in HaplotypeCaller right before the VariantContext gets written out to disk which partitions all the reads by which allele gave the read the highest likelihood. This will allow variants to be annotated by the refactored VariantAnnotator. Uninformative reads are mapped to Allele.NO_CALL --- .../org/broadinstitute/sting/utils/Haplotype.java | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) 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; } From 08fab49d303bb6e9553d8c14daab5d024aa15564 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 6 Apr 2012 15:56:01 -0400 Subject: [PATCH 04/14] Added function to get bases from the current base forward in the window in ReferenceContext --- build.xml | 4 ++-- .../sting/gatk/contexts/ReferenceContext.java | 10 ++++++++++ 2 files changed, 12 insertions(+), 2 deletions(-) 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/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(); From 52ef4a3e260200c869956632b11bf453aa29da93 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 6 Apr 2012 15:58:28 -0400 Subject: [PATCH 05/14] Function to compute whether a VariantContext indel is part of a TandemRepeat 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. 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. Note that in this context n is the base differences between the ref and alt alleles --- .../variantcontext/VariantContextUtils.java | 76 +++++++++++++++++++ .../VariantContextUtilsUnitTest.java | 72 ++++++++++++++++++ 2 files changed, 148 insertions(+) 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 2a121b6b0..c220a597b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -1201,4 +1201,80 @@ 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/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index ccf560f83..b5265f949 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 = ref; + 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); + } } From 45fc0ea98d02f887c6cee0677d5f0f449fac8a7b Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 6 Apr 2012 16:02:09 -0400 Subject: [PATCH 06/14] Improvements to indel analysis capabilities of VariantEval -- Now calculates the number of Indels overlapping gold standard sites, as well as the percent of indels overlapping gold standard sites -- Removed insertion : deletion ratio for 1 bp event, replaced it with 1 + 2 : 3 bp ratio for insertions and deletions separately. This is based on an old email from Mark Daly: // - 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 -- Added a new VEW argument to bind a gold standard track -- Added two new stratifications: OneBPIndel and TandemRepeat which do exactly what you imagine they do -- Deleted random unused functions in IndelUtils --- .../varianteval/VariantEvalWalker.java | 9 +++ .../varianteval/evaluators/IndelSummary.java | 59 +++++++++------- .../stratifications/OneBPIndel.java | 59 ++++++++++++++++ .../stratifications/TandemRepeat.java | 67 +++++++++++++++++++ .../sting/utils/IndelUtils.java | 33 --------- .../VariantEvalIntegrationTest.java | 31 +++++++-- 6 files changed, 194 insertions(+), 64 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java 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/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/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( From c22a66870c651aae082270313cce095e59bf9952 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 6 Apr 2012 16:27:20 -0400 Subject: [PATCH 08/14] Modified UnitTests to respect reference padding --- .../sting/utils/variantcontext/VariantContextUtilsUnitTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 b5265f949..107241beb 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -604,7 +604,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { private RepeatDetectorTest(boolean isTrueRepeat, String ref, String refAlleleString, String ... altAlleleStrings) { super(RepeatDetectorTest.class); - this.ref = ref; + this.ref = "N" + ref; // add a dummy base for the event here this.isTrueRepeat = isTrueRepeat; List alleles = new LinkedList(); From 87e6bea6c17e70057192479ed53b94db585ccf9b Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Sun, 8 Apr 2012 20:44:39 -0400 Subject: [PATCH 10/14] Adding engine capability to quantize qualities. * Added parameter -qq to quantize qualities using a recalibration report * Added options to quantize using the recalibration report quantization levels, new nLevels and no quantization. * Updated BQSR scripts to make use of the new parameters --- .../sting/gatk/GenomeAnalysisEngine.java | 12 ++++--- .../arguments/GATKArgumentCollection.java | 10 ++++++ .../gatk/walkers/bqsr/QuantizationInfo.java | 36 +++++++++++++++++-- .../recalibration/BaseRecalibration.java | 26 ++++++++------ .../BaseRecalibrationUnitTest.java | 2 +- 5 files changed, 66 insertions(+), 20 deletions(-) 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/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/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/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); From 6ddf2170b690c6f4c94e48cd5ecb7d1464de7958 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 9 Apr 2012 11:46:16 -0400 Subject: [PATCH 11/14] More efficient implementation of the sum of the allele frequency posteriors matrix using a pre-allocated cache as discussed in group meeting last week. Now, when the cache is filled, we safely collapse down to a single value in real space and put the un-re-centered log10 value back into the front of the cache. Thanks to all for the help and advice. --- .../AlleleFrequencyCalculationResult.java | 36 +++++++++++-------- .../genotyper/UnifiedGenotyperEngine.java | 10 +++--- .../broadinstitute/sting/utils/MathUtils.java | 10 ++++-- .../org/broadinstitute/sting/utils/Utils.java | 26 -------------- 4 files changed, 34 insertions(+), 48 deletions(-) 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/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index d4206e8ef..5d926a865 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 @@ -326,7 +326,7 @@ 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); } } @@ -369,7 +369,7 @@ 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(); @@ -380,7 +380,7 @@ 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 @@ -389,7 +389,7 @@ 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; @@ -424,7 +424,7 @@ 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); } 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. From ea4300d58373660a10c38750b3f74c2617f17db3 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 9 Apr 2012 13:45:17 -0400 Subject: [PATCH 12/14] Refactoring so that Unified Argument Collection doesn't use deprecated classes. --- ...ploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java | 2 ++ .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 4 ++-- .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 5 +++-- 3 files changed, 7 insertions(+), 4 deletions(-) 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 5d926a865..9241482d4 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 @@ -53,6 +53,9 @@ public class UnifiedGenotyperEngine { public static final int DEFAULT_PLOIDY = 2; + 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, @@ -622,8 +625,6 @@ 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; From f82986ee62cb2f65c31990798c0d4ff0bfa94e8d Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 9 Apr 2012 14:28:25 -0400 Subject: [PATCH 14/14] Adding unit tests for the very important log10sumLog10 util method. --- .../sting/utils/MathUtilsUnitTest.java | 12 ++++++++++++ 1 file changed, 12 insertions(+) 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);