diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreter.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreter.java
index 735bdc37c74..40d3685b23f 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreter.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreter.java
@@ -325,12 +325,13 @@ static VariantContext turnIntoVariantContext(final Tuple2<CpxVariantCanonicalRep
         return rawVariantContextBuilder.make();
     }
 
-    // TODO: 6/22/18 this leads to unnecessarily large file size, next PR trim it down to a single base like the case for DEL
     private static byte[] getRefBases(final ReferenceMultiSource reference, final CpxVariantCanonicalRepresentation cpxVariantCanonicalRepresentation)
             throws IOException {
         final SimpleInterval affectedRefRegion = cpxVariantCanonicalRepresentation.getAffectedRefRegion();
+        SimpleInterval refBase = new SimpleInterval(affectedRefRegion.getContig(), affectedRefRegion.getStart(),
+                                                                                   affectedRefRegion.getStart());
         return reference
-                .getReferenceBases(affectedRefRegion)
+                .getReferenceBases(refBase)
                 .getBases();
     }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractor.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractor.java
index b5fd7a3a553..3685dbe2004 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractor.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractor.java
@@ -15,6 +15,7 @@
 import org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData;
 import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig;
 import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments;
+import org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants;
 import org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
@@ -679,7 +680,7 @@ List<VariantContext> extract(final VariantContext complexVC, final ReferenceMult
                 }
 
                 // head and tail insertions only
-                extractFrontAndRearInsertions(complexVC, refSegments, altArrangement, result);
+                extractFrontAndRearInsertions(complexVC, refSegments, altArrangement, reference, result);
             }
 
             final String sourceID = complexVC.getID();
@@ -737,8 +738,8 @@ private static void whenAllSegmentsAppearAsIs(final VariantContext complexVC, fi
             }
             if ( idx + refSegments.size() - 1 < altArrangement.size() - 1 ) { // e.g. there's more after 1,2,3,4,..., there could be (that is, if long enough) front insertion
                 final SimpleInterval insertionPos = new SimpleInterval(complexVC.getContig(), complexVC.getEnd(), complexVC.getEnd());
-                final byte[] refBases = complexVC.getReference().getBases();
-                final Allele anchorBaseRefAlleleRear = Allele.create(refBases[refBases.length - 1], true);
+                final byte[] refBases = getReferenceBases(insertionPos, reference);
+                final Allele anchorBaseRefAlleleRear = Allele.create(refBases, true);
                 final VariantContextBuilder rearIns = getInsFromOneEnd(false, idx + refSegments.size() - 1, insertionPos,
                         anchorBaseRefAlleleRear, refSegmentLengths, altArrangement, true);
                 if (rearIns != null) result.add(rearIns);
@@ -805,9 +806,8 @@ static List<SimpleInterval> compactifyMissingSegments(final Set<SimpleInterval>
         }
 
         private void extractFrontAndRearInsertions(final VariantContext complexVC, final List<SimpleInterval> refSegmentIntervals,
-                                                   final List<String> altArrangement,
+                                                   final List<String> altArrangement, final ReferenceMultiSource reference,
                                                    final List<VariantContextBuilder> result) {
-            final byte[] refBases = complexVC.getReference().getBases();
             final List<Integer> refSegmentLengths = refSegmentIntervals.stream().map(SimpleInterval::size).collect(Collectors.toList());
             // index pointing to first appearance of ref segment (inverted or not) in altArrangement, from either side
             int firstRefSegmentIdx = 0; // first front
@@ -819,8 +819,8 @@ private void extractFrontAndRearInsertions(final VariantContext complexVC, final
                 }
             }
             if (firstRefSegmentIdx > 0) {
-                final Allele anchorBaseRefAlleleFront = Allele.create(refBases[0], true);
                 final SimpleInterval startAndStop = makeOneBpInterval(complexVC.getContig(), complexVC.getStart());
+                final Allele anchorBaseRefAlleleFront = Allele.create(getReferenceBases(startAndStop, reference), true);
                 final VariantContextBuilder frontIns = getInsFromOneEnd(true, firstRefSegmentIdx, startAndStop, anchorBaseRefAlleleFront, refSegmentLengths, altArrangement, true);
                 if (frontIns != null) result.add( frontIns );
             }
@@ -835,9 +835,10 @@ private void extractFrontAndRearInsertions(final VariantContext complexVC, final
             }
 
             if (firstRefSegmentIdx != altArrangement.size() - 1) {
-                final Allele anchorBaseRefAlleleRear = Allele.create(refBases[refBases.length - 2], true);
-                final SimpleInterval startAndStop = makeOneBpInterval(complexVC.getContig(), complexVC.getEnd());
-                final VariantContextBuilder rearIns = getInsFromOneEnd(false, firstRefSegmentIdx, startAndStop, anchorBaseRefAlleleRear, refSegmentLengths, altArrangement, true);
+                final int pos = complexVC.getEnd();
+                final SimpleInterval insertionPos = makeOneBpInterval(complexVC.getContig(), pos);
+                final Allele anchorBaseRefAlleleRear = Allele.create(getReferenceBases(insertionPos, reference), true);
+                final VariantContextBuilder rearIns = getInsFromOneEnd(false, firstRefSegmentIdx, insertionPos, anchorBaseRefAlleleRear, refSegmentLengths, altArrangement, true);
                 if (rearIns != null) result.add( rearIns );
             }
         }
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java
index 538be6f45d6..d3b74dd18a0 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java
@@ -289,7 +289,7 @@ public void testTurnIntoVariantContext() throws IOException {
         final CpxVariantCanonicalRepresentation cpxVariantCanonicalRepresentation = new CpxVariantCanonicalRepresentation(tig13846_3);
         final Tuple2<CpxVariantCanonicalRepresentation, Iterable<CpxVariantInducingAssemblyContig>> tuple2 =
                 new Tuple2<>(cpxVariantCanonicalRepresentation, Arrays.asList(tig13846_3, tig28220_5));
-        final byte[] refBases = TestUtilsForAssemblyBasedSVDiscovery.b38_reference_chr20_chr21.getReferenceBases(new SimpleInterval("chr20", 54849491, 54849615)).getBases();
+        final byte[] refBases = TestUtilsForAssemblyBasedSVDiscovery.b38_reference_chr20_chr21.getReferenceBases(new SimpleInterval("chr20", 54849491, 54849491)).getBases();
 
         final VariantContextBuilder baseVariantContextBuilder = cpxVariantCanonicalRepresentation.toVariantContext(refBases);
         baseVariantContextBuilder.attribute(GATKSVVCFConstants.TOTAL_MAPPINGS, 2);
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java
index 5b7ff05993b..3b08393ce2d 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java
@@ -141,7 +141,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 1.1: front insertion only
         SimpleInterval affectedInterval = new SimpleInterval("chr21:21264944-21265096");
         int svLen = 215;
-        String refAllele = "TATATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTCTGTGTATATATGTACACATATATACTATATATGTGTATGTGTATATATATACACACATATATTATATAT";
+        String refAllele = "T";
         String altSeq = "TATATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATATGTATATATACACATATATATTATATATATATGTGTCTGTATATATATACACATATATATTATATATATGTGTCTGTGTATATATATACACATATATATGTGTCTGTGTATATATGTACACATATATACTATATATGTGTATGTGTATATATATACACACATATATTATATAT";
         List<String> ctgNames = Arrays.asList("asm029034:tig00000","asm029034:tig00001");
         List<SimpleInterval> refSegments = Arrays.asList(new SimpleInterval("chr21:21264944-21264988"), new SimpleInterval("chr21:21264988-21265052"), new SimpleInterval("chr21:21265052-21265096"));
@@ -153,7 +153,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 1.2: rear insertion only
         affectedInterval = new SimpleInterval("chr20:61919906-61920109");
         svLen = 541;
-        refAllele = "TCGTGATTATGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGCGGTGATTGCATGGAAGTGTGGTGTCACAGTGATTGCGTGGAAGCGTGTCGTGATTGTGTGGAAGCATGGTATCGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCATGTTGTGATTG";
+        refAllele = "T";
         altSeq = "TCGTGATTATGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGCGGTGATTGCATGGAAGTGTGGTGTCACAGTGATTGCGTGGAAGCGTGTCGTGATTGTGTGGAAGCATGGTATCGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTGTGATTGTGTGGAAGCATGGTATCGTGATTGTGGAAGCGTGGTATCGCGGCGATTGTGTGGAAGCGTGGTGTCGCAGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGTGTGGAAGCATGGTGTCGTGATTGTGTGGAAGCATGTCGTGATTGTGTGGAAGTGTGATGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGGAAGTGTGGTGTCACGCTGATTGCATGGAAGTGTGTTGTGATTGTGTGGAAGCGTGATATCGCAGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATCGGAAGCGTGGTGTTGCGGTGATTGCATGGAAGCATGTTGTGATTGTGTGGAAGCATGGTATCGTGATTGTCTGGAAGCATGGTGTCATGGTGATTGGAAGTGTGTCGTGATTG";
         ctgNames = Arrays.asList("asm028707:tig00000");
         refSegments = Arrays.asList(new SimpleInterval("chr20:61919906-61919908"), new SimpleInterval("chr20:61919908-61920054"), new SimpleInterval("chr20:61920054-61920109"));
@@ -165,7 +165,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 1.3: front and rear insertion
         affectedInterval = new SimpleInterval("chr20:38653054-38653283");
         svLen = 485;
-        refAllele = "TGGTGGTGGTGGTGATGGAAATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGATGGTGGTGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTGGTGATGATGGTGATG";
+        refAllele = "T";
         altSeq = "TGGTGGTGGTGGTGATGGAAATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGATGGTGGTGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGGTGATAATGATGGTAGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGGTGATGGAAATGATGATGATGTTAATTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGATGGTGATGATGATTATGATGGTGGTGGTGGTGGTGGTGGTGCTGGTGATAGTGGTGGTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGGTGTTGGTGGTGCTGGTGATGATAATCATGCTGGTGGTGGTGGCGTTGATGATGGTGACAGTAGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTGGTGATGATGGTGATG";
         ctgNames = Arrays.asList("asm028418:tig00000");
         refSegments = Arrays.asList(new SimpleInterval("chr20:38653054-38653113"), new SimpleInterval("chr20:38653113-38653145"), new SimpleInterval("chr20:38653145-38653179"), new SimpleInterval("chr20:38653179-38653273"), new SimpleInterval("chr20:38653273-38653283"));
@@ -180,7 +180,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 2.1: both as-is and inverted, hence no inversion
         affectedInterval = new SimpleInterval("chr20:23122561-23122996");
         svLen = -293;
-        refAllele = "CTGTCATGTCACCGTGTGGGAGGGCTTGCAGGTGAAGTGGTCTGGGAGGGGTCCCCCAGACAAAGCCAAGGTTCTGAGAGTTGGCCCGAACACTGCTGGATTCCACGGCGGGGGCTTGGGACAGCCGGACTCAGAGACAGTAGGAGGTGACAATGTATATACATCACAATGATCACAATATAGCCCCACACGTGCCTTCCCCACCAACAGTCAGCTTGCCATGTCCCTTCCCCGACATCCCCATCTTAGTCCCAACACAGAGGCTCCCTCTGCCCTGTGTCTGTTTAGCCAGGATGCCACGGTTCTTCCCCCTTCTCCCATGTCCTCCTCCACACACCCTTCAAGGGCAACCCCAGAGATTTCTCCTCCATGATTTCTAAAGTCAGTGGTAAATCTGTTCCTCTTTAAAATCTCATCACACTGTTCACCACTTCCC";
+        refAllele = "C";
         altSeq = "CTGTCATGTCACCGTGTGGGAGGGCTTGCAGGTGAAGTGGTCTGGGAGGGGTCCCCCAGACAAAGCCAAGGTTCTGAGAGTTGGCCCGAACACTGCTGGATTCCACTTCACCTGCAAGCCCTCCCACACGGTGACATGACAGC";
         ctgNames = Arrays.asList("asm028059:tig00000","asm028059:tig00001");
         refSegments = Arrays.asList(new SimpleInterval("chr20:23122561-23122596"), new SimpleInterval("chr20:23122596-23122666"), new SimpleInterval("chr20:23122666-23122996"));
@@ -192,7 +192,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 2.2: no as-is but with inverted, but too short (coordinate and allele massage, original event CPX_chr20:34732145-34733344)
         affectedInterval = new SimpleInterval("chr20:34732145-34733344");
         svLen = -1139;
-        refAllele = "GCTTCATTTTTTTTCATTTGTCCAACAGGAATAAAAATATCTGCTCTCCTGACTTCCTGTGGTTATTGCAAGAAGCAAATAAGGCAATTGCTGTGAAATGATTTGGAAAATAAGCATCCTCCAAATGCAAAGAAGTGTTATTATTTAACAGAGTTTTCTGACTCTAGTTAGGAACTCATCCCATTGACTTTAGAATTGACATGAAAATTTATGCTTATATCCCTGCCTGTAAATAATACTTACTCTTTTGATCCATTTAAATTTTAACATAATCTCAAACTTACAGATGAGTCGCAAAAATGGTACCTTTACCTAGCTTTCCCACGTGTTTATATTGTGCCTAATTTTGTATATATTTCTGAATTATTCAAGAATAAACTGGTGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACCTGAGGTCAGGAGTTAGAGACCAGCATGATCCACATGGTGAAAACCCGCCTCTACTAACAATACAAAATTAGCTGGACGTGGTGGCACATGTCGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCATTGCACTCCAGCCTAGGCAACAAGAGTGAAACTCCGTATCAAAAAAAAAAGAGTAAACTGGAGATAATGTGTGCTTTACCAGTCCACAGGGAGTTCAACCCTGTTAACATCTTGATTTCAGCCCAGTGAAACTGGCTTCATCCTCCTGACCTTCAGAGCGATAAGAAAATAAATGTGTGTTATTTTAAGCCACCAAATTTGTGGTAATTCACCATAGCAGCCGTAGGAAACGAATATAGTCCATAATCAAATTTTGGCAATTGTCTAAATAGTATTCATTTAACCCATTTCAGTTCTCAAGATAATTTTCAATTCAGGATCATATTTTTTCAATTCAGGATCATGTGTTTTTAGTCTAATCTGGAACAGTTCTCCAGCCTTACTTTGTCTTTCTTGACTTGGACATTTTTGGAAAGTACAGCTATTGGCCACATGTGGTGCCTCATGCCTGTAATCTCAATACTTTGGGAGACTGAGGAGGGAGGATCACCTGAGGCTAGGAGTTCAAGACCAGCCTGGCCAACGTGAGGAACCCCCCCGTCTCTACTAAAAATACTCAAGATCCACCTGGACAA";
+        refAllele = "G";
         altSeq = "GTTGTCCAGGTGGATCTTGAGTATTTTTAGTAGAGACGGGGGGTTCAATTAACTCTTCCAA";
         ctgNames = Arrays.asList("asm010456:tig00000");
         refSegments = Arrays.asList(new SimpleInterval("chr20:34732145-34733303"), new SimpleInterval("chr20:34733303-34733342"), new SimpleInterval("chr20:34733342-34733344"));
@@ -204,7 +204,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 2.3: no as-is but with inverted, and inverted sequence long enough
         affectedInterval = new SimpleInterval("chr21:26001843-26002386");
         svLen = -1;
-        refAllele = "ATCACATCTAGGCATGGCTTTGAGCTTCACAGGCCAGAAGCTGCTCTGTCAGTAACTCAGAGGGGATATGGTCCCTAGACCCAATTCACTTTTAATAAATCAGGGTGCCAGTCCTTTAATTTTGGAAGATAAATAAAATTGCGAAGTAGATGGGATACTTACGTCAACAAGTTGGTTGGGTTTCATCCTGTAAGAGTATTGTGTACAGAAATCCAATTTGCTTTGGGAGCGTGGACTTTGAAAGCAGCAGTACTGAGTGAGATGGCCTTAATGATGGATGATAATGAGGTTGATGCTTTCGTAGCCACGTTTCCATCTGAAAACCACGTGAAGAGTGTCAGATCATCTTCATGTCCGTTGCATGGCGCATTTCTCCTGCGGAGTGTTTGACACCTTCTGGGCTTAGTGCTGACTGTCCCTCCTGTTGACATCATCGTGATGGTAGCCACCTCTGGTTTTACCAGTACTTTATTGCATCTACTGAAAGAGCAACGTGTATAGGGAAGTAAAACAATAGTTAGTCCCCATTTGTATTGACATTGTG";
+        refAllele = "A";
         altSeq = "ACAATGTCAATACAAATGGGGACTAACTATTGTTTTACTTCCCTATACACGTTGCTCTTTCAGTAGATGCAATAAAGTACTGGTAAAACCAGAGGTGGCTACCATCACGATGATGTCAACAGGAGGGACAGTCAGCACTAAGCCCAGAAGGTGTCAAACACTCCGCAGGAGAAATGCGCCATGCAACGGACATGAAGATGATCTGACACTCTTCACGTGGTTTTCAGATGGAAACGTGGCTACGAAAGCATCAACCTCATTATCATCCATCATTAAGGCCATCTCACTCAGTACTGCTGCTTTCAAAGTCCACGCTCCCAAAGCAAATTGGATTTCTGTACACAATACTCTTACAGGATGAAACCCAACCAACTTGTTGACGTAAGTATCCCATCTACTTCGCAATTTTATTTATCTTCCAAAATTAAAGGACTGGCACCCTGATTTATTAAAAGTGAATTGGTTCTAGGGACCATATCCCCTCTGAGTTACTGACAGAGCAGCTTCTGGCCTGTGAAGCTCAAAGCCATGCCTAGATGTGAG";
         ctgNames = Arrays.asList("asm029075:tig00000");
         refSegments = Arrays.asList(new SimpleInterval("chr21:26001844-26002384"), new SimpleInterval("chr21:26002384-26002386"));
@@ -219,7 +219,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
 
         affectedInterval = new SimpleInterval("chr21:23428920-23429023");
         svLen = 131;
-        refAllele = "TTTATATAAATATATATAAATATATAATATATAATAATATAATATAATATATATATAATATAATATAATATAATATATAATATATATTACATAATATATTATAT";
+        refAllele = "T";
         altSeq = "TATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATAATATATATAATATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATAT";
         ctgNames = Arrays.asList("asm029052:tig00000","asm029052:tig00001");
         refSegments = Arrays.asList(new SimpleInterval("chr21:23428920-23428968"), new SimpleInterval("chr21:23428968-23428998"), new SimpleInterval("chr21:23428998-23429023"));
@@ -235,7 +235,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 4.1: insertion length not big enough (coordinate and allele massage, original event CPX_chr10:13062977-13063278)
         affectedInterval = new SimpleInterval("chr20:13062977-13063278");
         svLen = 72;
-        refAllele = "CTGACCAATCAGCACCCTTGGCTCACTGGCTTACCGATTTCATCTCTGACCAATCAGCACTCCTGGCTCACTGGCTTACCAATTTCATCTCTGACCAATCAGCACTCCTGGCTCACTGGCTTACCCCCACCCACCAAGTTATTTTTAAAAACTTTGCTCCCCGAATGTTCGGGGAGACTGATTTGAGTAATAACAAAACCCTGGTCTCCCACACAGCCGGCTCTGTGTGAATTACTCTTTCTCTATTGCAGTTCCCCTGTCTTGATTTATCAGCTCTGTCTAGGCAGTGGGCAAGTTGAACC";
+        refAllele = "C";
         altSeq = "CTGACCAATCAGCACCCTTGGCTCACTGGCTTACCGATTTCATCTCTGACCAATCAGCACTACTTGCCCACTGCCTAGACAGAGCTGATAAATCAAGACAGGGGAACTGCAATAGAGAAAGAGTAATTCACACAGAGCCGGCTGTGTGGGAGACCAGGGTTTTGTTATTACTCAAATCAGTCTCCCCGAACATTCGGGGAGCAAAGTTTTTAAAAATAACTTGGTGGGTGGGGGGTAAGCCAGTGAGCCAGGAGTGCTGATTGGTCAGAGATGAAATTGGTAAGCCAGTGATCCAGGAGTGCTGATTGGTCAGAGATGAAATCGGTAAGCCAGTGAGCCAGGAGTGCTGATTGGTCAGCACCCTTGGTAACCAC";
         ctgNames = Arrays.asList("asm016524:tig00000");
         refSegments = Arrays.asList(new SimpleInterval("chr20:13062977-13063037"), new SimpleInterval("chr20:13063037-13063272"), new SimpleInterval("chr20:13063272-13063278"));
@@ -249,19 +249,19 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         // case 4.3: rear insertion only (coordinate and allele massage, original event CPX_chr22:36680290-36680686)
         affectedInterval = new SimpleInterval("chr21:36680290-36680686");
         svLen = 318;
-        refAllele = "TTCATGATCACTGCCACCTGCATCATGGCTATAATTACCACCGCCATCACCATCATCACTACCACCATCATCACCATCATCACCATTACCACCACCATCACTGCCACCATCACTACCACCATCATCACCATCATCACCACCACCACCATCACCACCATCACCATCACCACTTTCATCACCACCATCTTTATCACAGTCATTATTACCACCATCAATCATCACCACCTTCATGATCACTGCCACCTGCATCATGGTTACAATTACTACCACCACCATCAGCACCACCTTCATGATCACCACCACCTGCATCATGGCTATAATTACTACCACCATCACCACCACTAACACCACCATCATTATCACCACCATCACCACCATCTTCATGATCACTGCCACC";
+        refAllele = "T";
         altSeq = "TTCATGATCACTGCCACCTGCATCATGGCTATAATTACCACCGCCATCACCATCATCACTACCACCATCATCACCATCATCACCATTACCACCACCATCACTGCCACCATCACTACCACCATCATCACCATCATCACCACCACCACCATCACCACCATCACCATCACCACTTTCATCACCACCATCTTTATCACAGTCATTATTACCACCATCAATCATCACCACCTTCATGATCACTGCCACCTGCATCATGGTTACAATTACTACCACCACCATCAGCACCACCTTCATGATCACCACCACCTGCATCATGGCTATAATTACTACCACCATCACCACCACTAACACCACCATCATTATCACCACCATCTTCATGATCACTGCCACCTGCATCATGGCTATAATTACCACCATCATCACCACTATACTACCACCACCATCACCACAACCATCGCTACCACCACCACCACCACCATCACCATCATCACCATCACTACTACTGCCACCACTACCAAAACCACCACCACCACCATCACCACCACCATTGCCACCACTACCATCACCACCATCACCACCATCACCATCACCACCACTACCACCATTACCACCACCACCACCACCACCACCACCATCACCACCACCACCACCATCATCACCACTATC";
         ctgNames = Arrays.asList("asm029759:tig00000","asm029759:tig00001");
         refSegments = Arrays.asList(new SimpleInterval("chr21:36680290-36680331"), new SimpleInterval("chr21:36680331-36680659"), new SimpleInterval("chr21:36680659-36680686"));
         altArrangements = Arrays.asList("1","2","1","UINS-249");
         complex = makeTestComplexVariant(affectedInterval, svLen, refAllele, altSeq, ctgNames, refSegments, altArrangements);
-        expectedSimple = Arrays.asList(makeInsertion("chr21", 36680686, 36680686, 250, Allele.create("C", true)).attribute(EVENT_KEY, "CPX_chr21:36680290-36680686").attribute(CONTIG_NAMES, ctgNames).make());
+        expectedSimple = Arrays.asList(makeInsertion("chr21", 36680686, 36680686, 250, Allele.create("A", true)).attribute(EVENT_KEY, "CPX_chr21:36680290-36680686").attribute(CONTIG_NAMES, ctgNames).make());
         data.add(new Object[]{complex, b38_reference_chr20_chr21, multiSegmentsCpxVariantExtractor, expectedSimple});
 
         // case 4.4: front and rear insertion (coordinate and allele massage, original event CPX_chr19:8888822-8895655)
         affectedInterval = new SimpleInterval("chr20:8888822-8895655");
         svLen = -6179;
-        refAllele = "GCTTTTGGGATCAGGGCGGTAGGTGCAGATGGCATCCACTTTGGTGGCTGCCCCATCCTTCTTGGGCCTGGGGAGGGCAAGATTGGGGAAAGACAATACACGGATTGCCTAGGGAGGGGTTCTGAGATCCCACAGGGCAGGACAGGAGGGGGCCAGAGGAAATGAGAAGCCTGGTAGAGAAGTGAGAAGCCATACTTCCATTCTCTGAGTGCACTGACTCTTAGCAACTATGAGCAGAATCATGGATGCAAGGATTTTTATAAAATTGCAAAGTGGAAACTGCATTCTTGTAGCATGGGGTAAGGAGAACTCATACTTGAGACAGGTGAAGAGCTAGGTTTGGGGATGAAAGCAAGTGGACGAGGCATGTTTTTCTTGGGAGAAATCCTGGGAACAGAATTGAACCACTTGTGGAAAGGCAGGTAGGGGAAAGGAGGGAATTCAGAGGGATGACCAAGGTAGAAGCTCAGTCCTGCTGATGGGCTCTGCATCTCTCAGTTGAGGTGGGAGGTGGTGGGAACAGGAAGCACATTGGTCTTAGAGCCACTGCCTCCTGGATTCCACCTGGCTGCGGACATCTCCAGGGAGTGCAGAAGGGAAGCAGGTCAAACTGCTCAGATCAGTCAGACTGGCTGTTCTCAGTTCTCACCTGAGCAAGGTCAGTCTGCAGCCAGAGTACAGAGGGCCAACACTGGTGTTCTTGAACACAGGCCTGAGCTGTGGAGGAGGGAGAGGGAGGTGAGTGGGAGGACTGAAGTCATAGGGGTGTGGTAGAAGGGAGGTGGGCAGGGCTGGCAACAGTTGGTGGGGCTGGCATCAGTGGTTGGGGTATGCATATCTGGGGGCAAGATGAGGTAGATGAGATCTTCCATGCTCTGCAATAGGTGAGGTGGGCAGGACTAAACATGGTGAGTGGGGTAGAATGAGGTATGTGGGGCTCTTACCAGACCCTGAAGGACTCTCTCCGTGGTGTTAAACTTTCTAGAGCCAGGGTGATGCATGTTCTCCTCATACCGCAGGTTAGTGATGGTGAAGTTAATTGTGAATAGCACCAGGAGAGGGCTGGCGGCTATAGTGAAGATGGGAAATAAACAGTGTTCAAAAGTAGACTAACACTTAAGAATTTGTGATAGAATTGTTTCTAAACATATGCAACATGATTTAAAGTGACAAAATAAAAGGTTTTCACGCCTCCCTTCACTGTAATGGTACATAGTTCTCATAGAGCATACTAAATAATAGTAGTTAGATGCTAAGCACAGCTCTTGGTGCATATTCAGTATTCCATACTACTAGACATTATCTACTACCTTTGCCAACACCACGATCATCATCAACATCAGCAACACTGTGACCATCGCTATCATTATTGTCATCACCACCAGCATCAGCACCAAAACCATGACCATCATAATCCCTATGATCCCCACCCATCATCATCATTACACCACCAGCACCACAACCATCATCATCCATATAATCACCACTAGCACATGGTCACTAACACCATTATCATATCATTCTTACTATCATAACCACCATCACCACCAACATCATTATCATCATCACCACCATCATTATCCTCATTGTCAACATCATGATCACATTGTCAATTGCCATCAGAACCATCACATCACCACCACCACTATCATCCTTCCCATAATCATCACCACCACTATCATCATCATCACCATCAAAACCACTACCACCATCATCATCATCATCACCATCATCAGCAACACCATCATTGTTGTCATCATGTCCATCATCCCTATCATTATCATCATCATCACAACAATATAACCTTCCTGAGGATAGAGATTTTTATTTCTTTTGTGTTCCCTGCCTTATCCCTAGGGCCCCGAAGAAGCCAGACGCTCAACAAAATTTGTCGGTTGACTTGTCATCACTAGATTCACTAGGACTTTTCATTTTTATTTGAGTGAAAATGGTGGAGTTGTAGGCCAGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGGGGCCAAGGCAGACAGATCACGAGGTCAGGAGTTCGAGATCAGTTTGACCAATATGGTGAAGCTCCACCTCTACTAAAAATATAAAAATTAGCTGGGCATGGTGGCATGCACCTGTAATCCCAGCTACTCAGGAGGTGGAGGCAGGAGAATCGCTTGAACCTAGGAGGCAGAGGTTGCAGTGGGCTGAGATCACGCCATTGCATTCTAGCCTGGGTGACAGAGCAAGACTATGTCTCAAAAAAGAAAAAAAAGAAAGAAAAGAAAATGGCAGAGATGTTGACACTCCTCAGGCATGCTGTAATAGAGATGACACTGAATAGTACTCACTCATGGGTCCAGACAGGGAGGCTGGAGTTCTCGAGGTTGCCAGGTGCATTGTGGAGGTATCAGGAGCTGAGGAGAAGGTTTGCTGTATTAGTGAAAGCAGCAAACCCTCTCATGGCAGAAACACCAGCAGGTAGGAGTATTTATGGCCCTTGCTGCATGTGGGGCAGTATCTCCATCTGGAGCTGGGCCAGAGGGAAAGGGGAATAACTTGTGCTCTCTCTTCCTTCCCTCATGAAGAGGATATAGGGGCATAGAAGGAGAGGTAAGCTCCTGCCCTTTATGATGTAGGATCAGGAGCACTGGAACATCAGTTAATACTCACTTCTGGTGGTCGTCATAGAGCTCTGATGGGTGAAACCTGCATTGAGATGGAGGGACGAGAGTGGGTAAGTGTTAAGGGAGTGGTGGGGTACCCTGGTGCAACAGAAGGAATTTCCCAGAACACGGGCCATTGAAGATTCTCTATCAGCACCCTCAGATTTAGAAAGCAGATCCTGAGGGTAAATTCAGTTTGAGATGAAGAAGAAACCACGAAGTTTTGACCTTAGCCACCACATACAGACAACATGGTTGAGCCTTCAATAGCCAGACGGGAAGTGTGACCTCAGGCCAGAGAATAGAGGCTGTCCAGCAAGGAGGAAGAGACTCCAACCACATCAAAGTTGCTCACCATTGACATAGAGACTGTGCCTGTCCAGGGTGTAGGGGCCCAGCTCAGTGATGCCGTGGGTCAGCTGGCTCAGCTTCCAGTACAGCCGCTCTCTGTCCAGTCCAGGGCTTTTGGGGTCAGGACGATGGGTGCAGACAGCATCCACTCTGGTGGCTGCCCCATCCTTCTCAGGCCTAGGGAGGGCAGATGAAGCAAATAACAATTTAAAAATTGCCTCAGGAGGAGTTCTGAGATTTCCTGGGGCCAGACAGGAAGGGGCCAGAGGAAATGAGAAGCCTGGGAAAGAGGTAATAAGTCACATTTAGATTCTCTGAGTGTCCCGGCTGCCAGCCAGCCCAGGACTGTGAACAGAGTCATAGATGCAAGAACTTTTTATAAAATTGCAAAGTAAAGCCTGCATTCTCATGGCATGGAGACAAGAGTACTCAGACATGAGACAGATGAAGAGCTGGAATTGGGGATGAAAGCAAGTGGATGAGGCATGCTTGTCTTGTGAGAAATCCTGGGGACAGAATTTAACAACTGGAGGAAAGGGAGGTGGGTGGAAAGGAGGGAATTCAGAGGGATGACCAAGGTAGAAGCACAATTCTCCTCATGGACTCTGCAGAATCTCGCAGTTGATTGGGGTGGTGCTGATGGTATCAGGAGACAGATTAGTTTTGAAGCCAATGCTTCCCGAATTCCATCTGTTGTGAGGACATTCACAGGGATGGCAGGAAAAAAAAAAACAATCCAAACTCTTTGCGACTAGGAACAATTGGGGCAGCTAGGCTAGCTCTTCTAAAGTCTCACCTGAGCAAGGTCAGTCTGCAACCAGAGTACAGAGAGCTGACACTGGTGTTCTTGAACAAGGGCATAAGCTGTGGAAGAGGGAGAGGGAGGTGACTAGGAGGGCTGGGGATATAGTGGTGGGGCACAAGTGTGGCGAGTGCAGCTGGCACCAGTGGGCAGGGCTTGTGTCTCTAGGGGAGATGGATGAGATTTTCTTCCATGGCCCTGGCATGGGTGATGTTGTTGGGACCAGGTAACGTGGGAGGGGCAGAGTAAGTTGGACAGGGGTCTCACCAGACCCTGAAGGACCCTCTCCGTGGTGTTGAACTTCCTGGAGCCAGGGCGACGCATGTCCTCCTCATACTGCAGGTTAGTGATGGTAAAATTGAGGGTGAATGGCAGCAGGACAGGGCCAGTGGCTGTAGTAAAAGGTGTGGAAACAAACACTATTGTGTTTGTTTGTATTTTTAATCTGTTGCATATAGTTAAAAATAAGTCTATTGCAAACTCCTCAAGTTTCTCGACTTTTGCAATAGACTTGAAGAGTTTGCAATAAGTTTATTTTTAATCATATGCAACAGAATTTAAAATGAATGACAAAATTAAAGGTTTCCATGCCCTTCTTGATAGAAATTATTTTTTTAAAAAGCATATTACATAATATTTGTTAGATTCTGAGCCCAGCTTTTGGTGCATATTCAGTGCTGAAAAATATCAGATATTACCTGTTACCTTTGTCATCACCATTATCATCATCATCATCATCATCATCACCATTATTGTCAGCATCAGCACCAAGACCATCACCACAACGATAATCCCCATCAATACTACCACAAACATCATTATCACCATAGTCATATCATCATTACCATCATAATCATCATCACTGTCATTATCTGAATAATCATCATCACGATCATTGTCATCATAATCACTATCGCCATCACTATTGTCATCCTCACCATCACGAATGTCACAATCCACATCAACACCACCACAAACATCATCATCATCACCATAATCACATCATCATTAGCATCATAACCAGCAACATTACTGTCATCATCCAAACAACCATCATCATCTTTACCATCATTGTCACCATTGTTATCATCACCACTCCAACATCATCACCACAATCAACACAACCGTCATCATCATCATTATTATTATCATTATTGTCAAAATCCCCATAATTATTGTCAATTGTAATCCCCACCACCACCATCATTCTTCCCATGATTACCACCAGCATAATCATCATTATCCTTACCATCACCACCACCACCACCACCACTGCAATCATCATCACCGCCACCCCCATCATCATCATCATCACAATAATATAAGCTCACTGAGGGCAGTGTTTTTTCTTTTTTTGTTCCCTGATGTATATCCAGGTCCTGATACAGAGGCAGTGCTCAATGAACTGGGTTGGTTGACCTATGGTTACTACATTTACTATGAATTTCCATCTTTAGTTGAGTGAATAATGACAGAGATGTTTACACTCATCAACCATGCTCTAACAGAGTATAAACAGAGATGTTTACACTCATCAACCATGCTCCAAATACCATTGACTGGTATTTACCTGTGGGGCCAGGGAGGGATGATGGAGTCTCAGAGGTTTCCGGCTGTACTGTGAAAGTCCCAGGAGCTGAGGAGAAGCCCTCAACAGTGAAAGGAGCAAGTGCTCTCATGGAAGTAATGCCAGCAGGAGGGACTATTCATGGGGATTTTTGCCTGTGGGGCTTCAGCTGGGATTCTGATTAGCTGGGGCAGTGGGGAAGGGGAATAATTTGTGTCCTCTATGTTCCTTCCCTTATGGAAAGGACATAAGGGCTTATGAATAGGGGTCAGCTCCTGCTAAGTTTGTTGTAAGATTGGGGCCATGGGAACATCAGTAGAATACTCACTGCTGGTGGTGGGCACAGAGCTCCGCTGGGTGAAACCTGCATAGAGAGGGAGGGAGGAGTGTGGATAAGAGTCAAGGGGGAGGTAGGGGGTCAAAAAAAAGTCAGGGCTACCCTGGTGGAATGAAAGGAGTTTCATGGAACAGGGGCCTTTGGAGATTCTCTGTCAGAATCTGAGTATCAGGGAAGAAGCTACTAAGGATGAAATCAGTTCAAGATAAAGAAGAAATCATGAAATTCTGACATCAATCACCACATACAGACGTGTCCTAGCCTTCAGTGTCCAAGCAGGGCATGTGACCTCAAGTAAGAGAGTAGAGGCTGCCCAGGCAGGAGAAAGAGACTCTAATCACATCAGAGCTGCTTACCATTGACATAGAGACTGTCCCTATCCAGGGTGTAGGGTCCCAGCTCAGTGATGCTGTGGGTCAGCTGGCTCAGCTCCCAGTATAGCTGCTGTCTGTCTAGCCCAGGGATTTTGGGGTCAGGGCGGTGGGTGCAGATGGCGTCCACTCTGGTGGCTACTCCATCCTTCTCAGGCCTGGGGAGAGGTGGTGAGGGGAATGGCAATAAATGAATTGCCTAAGGAGAGGTCTTGAGATGGCAGAGTGTAGGACAAGAAGGACAGAGGAAGTAAAAAGTCTAATACAGAGGTGGGAAGCAATACTTAGATTCCCTGAGTGTACTGGACTGCTTGGGACTGTGAGCATAGTTGTGGATATAACAGTTTTCCCAAAATGGCAGGGTGGATCCTGCATTCTTAAAGCATGGAAACAGGAGAGCTCAGACTTGAGATAGCTGAAGAGCTGGAATTGGGGATGAAAACAAGTGGTTGAGGCATGTTTGTCTTGAGAGAAATCCTGGTTACAGAGTTTAACACCTAAAGTCAAGGGAGGTGGGGGGAAAACAGGGAATTCTGAGGAATGGCCAGGGCAGAAGTCCAGTCCTGTTGATGGACTCTGGAATCTCTCAGTCAGTTTGGAAGTGGGGGCGGGGGCACTGCTAATACCAGGAGACAGGTTAGTCCTGGAGCCAGTTTCCTGGATTCCATCTTTGATAAGAATAATCACAAAGAGGACAGGAAAAAAGAAGTCCAAACTCATTGAGACTAGGAATAATCGGGGCAGCCACACTGGAAATT";
+        refAllele = "G";
         altSeq = "GTTTAGAGGGTCAAGGCGGTGAGTGCAGATGGTGTCCACGCCGGTGGCTGCCCCACGTTTTTCAGGCCTGAGGAGGATAAGTGAGGGGAATGACAATAAGTGGATTGCCTAGGAAGAGGTCCTGAGATTCCTGAGGGAAGGACAGGCAGGGGCCAGAGGAAGTGGTACAGAGGTGAGAAGCTACACATAGATTCTGTGAGTGCACCAACTCCCAGCCAGCCTGGGTCTATGAGCAGAATCATGGACACAAAAATATTTGTAACATTATAAAGTGGATCCTCTGTTCTCAGAAGATGGGGACAGGAGAGCTCAGACTTGAGACAGGTGAAGAGCTGGAATTGGGGATCAAAGCAAGTGGATGAGGCATGTTTGTGTTTGAAAGAAATGCTGGTTGTAGAGTTTATTATCTGCAGGAAAGGGAGGTGGTGGGAAAGGAGGGAACTTAGAGGGATGACCAGGGTAGGGGCCCTATCCTGCTGATGAGCTCTGCAGCATCACTGTTGAGTGGAGAGATGTTACTATCAGGGACACTTTGGTCCTGGAGCCACTGCCTCCTGGATTCCACCAGTGCTGAGGGCACCCCTAGGGAGGGCAGGAAGGAAGTTTTCCAAACTTCTTGGGACTGGGAACAATTGGAGAAGGTAGGCTGGCTCCT";
         ctgNames = Arrays.asList("asm026939:tig00007");
         refSegments = Arrays.asList(new SimpleInterval("chr20:8888822-8895288"), new SimpleInterval("chr20:8895288-8895361"), new SimpleInterval("chr20:8895361-8895655"));
@@ -270,7 +270,7 @@ private List<Object[]> caseForMultiSegmentsCalls() {
         expectedSimple = Arrays.asList(makeDeletion(new SimpleInterval("chr20:8888822-8895287"), Allele.create("G", true)).attribute(EVENT_KEY, "CPX_chr20:8888822-8895655").attribute(CONTIG_NAMES, ctgNames).make(),
                                        makeDeletion(new SimpleInterval("chr20:8895361-8895654"), Allele.create("T", true)).attribute(EVENT_KEY, "CPX_chr20:8888822-8895655").attribute(CONTIG_NAMES, ctgNames).make(),
                                        makeInsertion("chr20", 8888822, 8888822, 298, Allele.create("G", true)).attribute(EVENT_KEY, "CPX_chr20:8888822-8895655").attribute(CONTIG_NAMES, ctgNames).make(),
-                                       makeInsertion("chr20", 8895655, 8895655, 281, Allele.create("T", true)).attribute(EVENT_KEY, "CPX_chr20:8888822-8895655").attribute(CONTIG_NAMES, ctgNames).make());
+                                       makeInsertion("chr20", 8895655, 8895655, 281, Allele.create("C", true)).attribute(EVENT_KEY, "CPX_chr20:8888822-8895655").attribute(CONTIG_NAMES, ctgNames).make());
         data.add(new Object[]{complex, b38_reference_chr20_chr21, multiSegmentsCpxVariantExtractor, expectedSimple});
 
         return data;
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/CpxVariantReInterpreterSparkIntegrationTest_complex.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/CpxVariantReInterpreterSparkIntegrationTest_complex.vcf
index ead20dec8ee..a12e4edaae9 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/CpxVariantReInterpreterSparkIntegrationTest_complex.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/CpxVariantReInterpreterSparkIntegrationTest_complex.vcf
@@ -41,26 +41,26 @@
 ##contig=<ID=chr20,length=64444167,assembly=38>
 ##contig=<ID=chr21,length=46709983,assembly=38>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-chr20	2379056	CPX_chr20:2379056-2379968	CTGCTGAAGGTCACACAGCCAGTTTGGCCCAGAGATAACAGAACCCAGGACTCTACTGCCAGGCTATGATGCTCACTTCTAAACTGAGTATGGGCCGGGTGCAGTGGCTCTCACTTGTAATCTCGCACTTTGGGAGGCTGAGGTGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACTGTCTCTACTTAAAATACACAAAAAATTAGCCGGGCATGGTGGCACACGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAAGTAGAGGTTGCACCGAGCTGAGATCGTGCCGCTGCACTTCACCCTAGGTGACAGAGCGAGACCCTGTCTCAAAAAAAAAAAACGAGGAGTATGAATTATTATTTGGGGTCTCGAGCAGTGGGGCAGGCAGTGATTTTGATGCCCTGTCTTCTGGGAGCTCCCGTCCAAGCAAGCCCAGGATGAAAGATAAAAGGGCCCTGAATAAGACCATCATTAGTGGGGAGGAGCCTGACCCTGCATAGGCAGAAAAGCAGCTTCAGCAGGGCCCAGGGTCTACAGGGCAGCAGCCTGCAGGGTGTTGAGGAAGGAGCTGCCCTGGGCTGCTGCCAGATGTCAGTAATTATAAGGCTATGTGGGTCTGCAGACAGCTCATTAAAGACGCTTGATCTGCGTGAAACCAGGAAGCAGAACTCAGCCTCTTTGCCACTTTCTGTAAGAAATCCAACCACATCAAACACTTTGGGGTTTTTATGCAGTTTCCTGAATGTTGGGGTGATCCCAGGGAGCGGCCTCATCCTACTGTGCTCAGCACACGGTTGTCTCCTTACCCTTCCTTGTCTCTTTCCCTCGATTCTACCCCCTCCCACTTCCCCTTCCTCACTGGCCCAG	<CPX>	.	.	ALIGN_LENGTHS=1401;ALT_ARRANGEMENT=1,2,3,UINS-4,1,3;CTG_NAMES=asm027854:tig00003;END=2379968;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1401;SEGMENTS=chr20:2379056-2379257,chr20:2379257-2379963,chr20:2379963-2379968;SEQ_ALT_HAPLOTYPE=CTGCTGAAGGTCACACAGCCAGTTTGGCCCAGAGATAACAGAACCCAGGACTCTACTGCCAGGCTATGATGCTCACTTCTAAACTGAGTATGGGCCGGGTGCAGTGGCTCTCACTTGGAATCTCGCACTTTGGGAGGCTGAGGTGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACTGTCTCTACTTAAAATACACAAAAAATTAGCCGGGCATGGTGGCACACGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAAGTAGAGGTTGCACCGAGCTGAGATCGTGCCGCTGCACTTCACCCTAGGTGACAGAGCGAGACCCTGTCTCAAAAAAAAAAAACGAGGAGTATGAATTATTATTTGGGGTCTCGAGCAGTGGGGCAGGCAGTGATTTTGATGCCCTGTCTTCTGGGAGCTCCCGTCCAAGCAAGCCCAGGATGAAAGATAAAAGGGCCCTGAATAAGACCATCATTAGTGGGGAGGAGCCTGACCCTGCATAGGCAGAAAAGCAGCTTCAGCAGGGCCCAGGGTCTACAGGGCAGCAGCCTGCAGGGTGTTGAGGAAGGAGCTGCCCTGGGCTGCTGCCAGATGTCAGTAATTATAAGGCTATGTGGGTCTGCAGACAGCTCATTAAAGACGCTTGATCTGCGTGAAACCAGGAAGCAGAACTCAGCCTCTTTGCCACTTTCTGTAAGAAATCCAACCACATCAAACACTTTGGGGTTTTTATGCAGTTTCCTGAATGTTGGGGTGATCCCAGGGAGCGGCCTCATCCTACTGTGCTCAGCACACGGTTGTCTCCTTACCCTTCCTTGTCTCTTTCCCTCGATTCTACCCCCTCCCACTTCCCCTTCCTCACTGGCCCAGTGAGGCTGCTGAAGGTCACACAGCCAGTTTGGCCCAGAGATAACAGAACCCAGGACTCTACTGCCAGGCTATGATGCTCACTTCTAAACTGAGTATGGGCCGGGTGCAGTGGCTCTCACTTGTAATCTCGCACTTTGGGAGGCTGAGGTGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACTGTGCCCAG;SVLEN=913;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	12558793	CPX_chr20:12558793-12558810	AAAAAAAAAAAAAAAAAA	<CPX>	.	.	ALIGN_LENGTHS=597;ALT_ARRANGEMENT=-chrX:99014092-99014129,UINS-101;CTG_NAMES=asm027960:tig00003;END=12558810;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=597;SEGMENTS=chr20:12558793-12558810;SEQ_ALT_HAPLOTYPE=AGACAAAGAAACAAACAAACAAAACAAAACTATATATATATATATATACACACACACACACACACACACATTATTAAAATTCAGATTTAAATAAACTGACTATAAAAAAGTACTTTTGAAACAAAAACTTTAATCATGATTATATATATTA;SVLEN=18;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	18675721	CPX_chr20:18675721-18675877	TATGTGTATATTTACACACATATATATGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACACATATATGTAAATATACCTATGTGTATATTTACACATATATATGTAAATATACCTATGTGT	<CPX>	.	.	ALIGN_LENGTHS=564;ALT_ARRANGEMENT=1,UINS-28,1,UINS-64,1;CTG_NAMES=asm028012:tig00004;END=18675877;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=564;SEGMENTS=chr20:18675721-18675877;SEQ_ALT_HAPLOTYPE=TATGTGTATATTTACACACATATATATGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCGATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTAAATATACCTATGTGT;SVLEN=157;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	20269131	CPX_chr20:20269131-20269199	ATATATATATATATATACACACACACACACACACATACATATATGTATATACACACACATATATACATA	<CPX>	.	.	ALIGN_LENGTHS=40;ALT_ARRANGEMENT=-chrX:137700299-137700331;CTG_NAMES=asm028026:tig00000;END=20269199;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=40;SEGMENTS=chr20:20269131-20269199;SEQ_ALT_HAPLOTYPE=ACACACACACACACACACACACACACACACACACA;SVLEN=69;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	23122561	CPX_chr20:23122561-23122996	CTGTCATGTCACCGTGTGGGAGGGCTTGCAGGTGAAGTGGTCTGGGAGGGGTCCCCCAGACAAAGCCAAGGTTCTGAGAGTTGGCCCGAACACTGCTGGATTCCACGGCGGGGGCTTGGGACAGCCGGACTCAGAGACAGTAGGAGGTGACAATGTATATACATCACAATGATCACAATATAGCCCCACACGTGCCTTCCCCACCAACAGTCAGCTTGCCATGTCCCTTCCCCGACATCCCCATCTTAGTCCCAACACAGAGGCTCCCTCTGCCCTGTGTCTGTTTAGCCAGGATGCCACGGTTCTTCCCCCTTCTCCCATGTCCTCCTCCACACACCCTTCAAGGGCAACCCCAGAGATTTCTCCTCCATGATTTCTAAAGTCAGTGGTAAATCTGTTCCTCTTTAAAATCTCATCACACTGTTCACCACTTCCC	<CPX>	.	.	ALIGN_LENGTHS=876,876;ALT_ARRANGEMENT=1,2,-1;CTG_NAMES=asm028059:tig00000,asm028059:tig00001;END=23122996;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=876;SEGMENTS=chr20:23122561-23122596,chr20:23122596-23122666,chr20:23122666-23122996;SEQ_ALT_HAPLOTYPE=CTGTCATGTCACCGTGTGGGAGGGCTTGCAGGTGAAGTGGTCTGGGAGGGGTCCCCCAGACAAAGCCAAGGTTCTGAGAGTTGGCCCGAACACTGCTGGATTCCACTTCACCTGCAAGCCCTCCCACACGGTGACATGACAGC;SVLEN=436;SVTYPE=CPX;TOTAL_MAPPINGS=2
-chr20	28561412	CPX_chr20:28561412-28561576	AACATCATATGTGACAGGCTGTCATAGTCACCATTCCCATGACCATAGTCATGGGAATCTTGCTCGTGTTACAGGGAAGCACTGTCCAACATCATATGTGACAGGTTCTCATCGTCACCATCATCATGGGAATCTTGTGCATGTTACAGGGAAGCATTGTCCTAC	<CPX>	.	.	ALIGN_LENGTHS=416;ALT_ARRANGEMENT=UINS-74,1,UINS-74;CTG_NAMES=asm008294:tig00014;END=28561576;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=416;SEGMENTS=chr20:28561413-28561575;SEQ_ALT_HAPLOTYPE=AACATCATATGTGACAGGCTCTCATAGTCACCATCATCACAGAAATCTCGCGCATGTTACAGAGAAGCACTGTCCTACATCATATGTGACAGGCTCTCATAGTCACCATTCCCATGACCATAGTCATGGGAATCTTGCTCATGTTACAGGGAAGCACTGTCCAACATCATATGTGACAGGCTCTCATCGTCACCATCATCATGGGAATCTTGTGCATGTTACAGGGAAGCATTGTCCTACATCGTATGTGACAGGCTCTCATAATCACTATCATCATGGGAATCCTGTGCATGTTACAGGAAAGAACTGTCCTGC;SVLEN=165;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	38123803	CPX_chr20:38123803-38124181	ACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATA	<CPX>	.	.	ALIGN_LENGTHS=1516,1516;ALT_ARRANGEMENT=1,2,3,UINS-5,1,UINS-531,3,4,3,4;CTG_NAMES=asm028411:tig00000,asm028411:tig00001;END=38124181;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1516;SEGMENTS=chr20:38123803-38123868,chr20:38123868-38124004,chr20:38124004-38124014,chr20:38124014-38124181;SEQ_ALT_HAPLOTYPE=ATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATA;SVLEN=379;SVTYPE=CPX;TOTAL_MAPPINGS=2
-chr20	38653054	CPX_chr20:38653054-38653283	TGGTGGTGGTGGTGATGGAAATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGATGGTGGTGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTGGTGATGATGGTGATG	<CPX>	.	.	ALIGN_LENGTHS=1534;ALT_ARRANGEMENT=1,2,3,4,3,1,2,3,4,5,2,3,4,5;CTG_NAMES=asm028418:tig00000;END=38653283;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1534;SEGMENTS=chr20:38653054-38653113,chr20:38653113-38653145,chr20:38653145-38653179,chr20:38653179-38653273,chr20:38653273-38653283;SEQ_ALT_HAPLOTYPE=TGGTGGTGGTGGTGATGGAAATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGATGGTGGTGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGGTGATAATGATGGTAGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGGTGATGGAAATGATGATGATGTTAATTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGATGGTGATGATGATTATGATGGTGGTGGTGGTGGTGGTGGTGCTGGTGATAGTGGTGGTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGGTGTTGGTGGTGCTGGTGATGATAATCATGCTGGTGGTGGTGGCGTTGATGATGGTGACAGTAGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTGGTGATGATGGTGATG;SVLEN=230;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	47895195	CPX_chr20:47895195-47895581	AAGGGTCCGGAAGCTGGCGACCCAGGGAGGAGAGGTCTTGTTCTATTGTGAGGGTCGTGGAGCTGCCGACCCAGGGAGGAGCAATTTTGTTGTAATTTGAGGGTCCGGAAGCTGGCGACCCAGGGAGGAGAGGTCTTGATCCGGTCTGAGGGTCGTGGAGCTACAGACCCAGGGTGGAGCAATGTTGTTGTAGTTCGAGGGTCTGGTAGCTGGCAACTTGGGGAAGACAAGTCTTGTTCGAGTTCGAGGGTCGTGGAGCTGCAGACCCAGGGAGGAGCCATTTTGTTGTAGTTCAAGGGTCCGGAAACTGGCGACCCAGGGAGGAGAGGTCTTGTTCTAGTTTCAGGGTCGTGGAGCTTCTGACCCAGGGAGGAGCATTGTTGTTTT	<CPX>	.	.	ALIGN_LENGTHS=289;ALT_ARRANGEMENT=2;CTG_NAMES=asm028508:tig00005;END=47895581;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=289;SEGMENTS=chr20:47895195-47895294,chr20:47895294-47895482,chr20:47895482-47895581;SEQ_ALT_HAPLOTYPE=AAGGGTCCGGAAGCTGGTGACCCAGGGAGGAGAGGTCTTGATCTGGTCTGAGGGTCGTGGAGCTACAGACCCAGGGAGGAGCAATGTTGTTGTAGTTCGAGGGTCCGGTAGCTGGCAACCCGGGAAAGAGAAGTCTTGTTCGAGTTTGAGGGTCGTGGAGCTGCAGACCCAGGGAGGAGCAATTTTGTTGT;SVLEN=387;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	51740560	CPX_chr20:51740560-51740561	AT	<CPX>	.	.	ALIGN_LENGTHS=1104,1104;ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496;CTG_NAMES=asm028558:tig00002,asm028558:tig00003;END=51740561;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1104;SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGT;SVLEN=2;SVTYPE=CPX;TOTAL_MAPPINGS=2
-chr20	51740560	CPX_chr20:51740560-51741035	ATTTTGTGTTGTTGTTTTTGTTTTTTGAGACAAGGTCTCATTCTGTCACCCAGGCAGGACTGTGGTGGCACCATCATGGCTCAGCGCAGCCTCCTTTTCCCCAGGCTCAAGTGATCCTCTTGCCTCAGCCTCCCACGTGGCTGGGACTACAGGTGTGTACCACCACTCCCGGATAATTTTTTTTATTTTTTATTTTTAGTAAAGACAGTCTCACTATGTTGCCCAGGCTGGTCTCCAACTCCTGGTCTCAAGCAATCCTCCCAGTTCAGCCTCTCAAAGTGCTGGGATTACAGATGTGAGCCACAATACCCGGCCCCAATTCTAATGTTTAAAGAGTACAGTCTACACCTTAAAGCCTGCATTTTATCATCCTGTCCTCACTGCTCTGACTTCTTTACAGTTGTGCTGTCCACCTTGGCGGCTTCTACCACATGTGGCTATTTTAAGTTTCAATTAATTAAAATTAAATTTTAATT	<CPX>	.	.	ALIGN_LENGTHS=895,895;ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496,1,UINS-49;CTG_NAMES=asm028558:tig00000,asm028558:tig00001;END=51741035;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=895;SEGMENTS=chr20:51740561-51741034;SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGTTTTGTGTTGTTGTTTTTGTTTTTTGAGACAAGGTCTCATTCTGTCACCCAGGCAGGACTGTGGTGGCACCATCATGGCTCAGCGCAGCCTCCTTTTCCCCAGGCTCAAGTGATCCTCTTGCCTCAGCCTCCCACGTGGCTGGGACTACAGGTGTGTACCACCACTCCCGGATAATTTTTTTTATTTTTTATTTTTAGTAAAGACAGTCTCACTATGTTGCCCAGGCTGGTCTCCAACTCCTGGTCTCAAGCAATCCTCCCAGTTCAGCCTCTCAAAGTGCTGGGATTACAGATGTGAGCCACAATACCCGGCCCCAATTCTAATGTTTAAAGAGTACAGTCTACACCTTAAAGCCTGCATTTTATCATCCTGTCCTCACTGCTCTGACTTCTTTACAGTTGTGCTGTCCACCTTGGCGGCTTCTACCACATGTGGCTATTTTAAGTTTCAATTAATTAAAATTAAATTTTAATTTAATTAATTAAAAATAAATTTTAATTAATTAATTAAAAATAAATTTTAAT;SVLEN=476;SVTYPE=CPX;TOTAL_MAPPINGS=2
-chr20	54849491	CPX_chr20:54849491-54849615	CAAATCTCATGTGAAATGTATCCCCAGTGTGGAGGGGGCAGATCCTCATAATGGCTTGGGCCCTTCCATGGTAATAGTGAGTCTTGCTCTGTAGTTCATAGAGAGCTGATTGTTAAAGGAGTCTG	<CPX>	.	.	ALIGN_LENGTHS=88;ALT_ARRANGEMENT=UINS-36,-chr14:58474127-58474172,UINS-54;CTG_NAMES=asm028586:tig00000;END=54849615;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=88;SEGMENTS=chr20:54849491-54849615;SEQ_ALT_HAPLOTYPE=CCAAATCTCATGTTGAAATGTAATCCCCAGTGTTGGAGGGGGGCAGATCCCTCATGAATGGCTTGGTGCCCTTCCCATGGTAATGAGTGAGTTCTTGCTCTGTTAGTTCATGAGAGAGCTGATTGTTTAAAGGAGTCTGG;SVLEN=125;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	58695019	CPX_chr20:58695019-58695020	GT	<CPX>	.	.	ALIGN_LENGTHS=82;ALT_ARRANGEMENT=UINS-72,chr20:58695237-58695339,UINS-83,chr20:58695287-58695340,UINS-12,chr20:58695229-58695328,UINS-27,chr20:58695237-58695320;CTG_NAMES=asm028638:tig00002;END=58695020;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=82;SEQ_ALT_HAPLOTYPE=TTGCGTGTGTATGAGTGCTGGTGTGTGCATGAATGGTGTGTGTGGTGTGTTTATGTGTGGTGTGTGTTGCTGTGTGAGTGCTGGTGTGTGCATGAGTGGCGTGTGTGTGGTGTGTGTTGCTGTGTGTGTATGAGTGTTGGTGTGTGCATGAGTGGTGTGTGTGTGCTGTGTGTATGTGTGGTGTGTGTTGCTGTGTATGAGTGTTGGTGTGTGCATGAGTGGTGTGTGTGTGCTGTGTGTACGTGTGTGTGTTGCTGTGTGTGTGTTTGAGTGCTGGTGTGTGCATGAGTGGTGTGTGTGTGGTGTGTGTGGTGTCTGTTGCTGTGTGTGTTTGAGTTCTGGTATGTGCATGAGTGGTGTGTGTGTGTGCTGTGTGTGTGGTGTGTTGCTGTGTGTGTATGAGTGCTGGTGTGTGCACGAGTGGTGTGTGTATTTGCGGTGTGTGTTGCTGTGTATATGTGAGTGCTGGTGTGTGCATGAGTGGCGTGTGTGGTGTGTATGTGTGGTGTGTGTTGCTGTTTGTGTTTGAGTGCTGATGTGTGCATGAGTGG;SVLEN=2;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	61375650	CPX_chr20:61375650-61376102	TGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTAGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGCTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGCTCTTGGTGCTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATACTGTGGTTTGTGGATGGTAGTGTGATGGTCTTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGG	<CPX>	.	.	ALIGN_LENGTHS=1559;ALT_ARRANGEMENT=1,2,3,2,1,2,3;CTG_NAMES=asm028687:tig00001;END=61376102;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1559;SEGMENTS=chr20:61375650-61375759,chr20:61375759-61375874,chr20:61375874-61376102;SEQ_ALT_HAPLOTYPE=TGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTAGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGCTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGCTCTTGGTGCTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGATGATAGTGGGGTTTATTGATGGTAGTGTGATGGTCTTGGTGGTGCTGATAATGGTGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTGGCGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGGTGATGATGTAGTTTGTTGATGGTAGCGTGATGTTCTTGGTGCTGGTGGTGGTGATGATGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGGTGGTGGTGATAGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGATGCTGGTGATGGTATTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTCGTGGTGGTGGTGTGGTTTGTCGATGGTAGTGTGGTGGTCTTGGTGCTGGTGGTTGTCGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGATGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTAGTGATGGTGTGGTTTGCTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATACTGTGGTTTGTGGATGGTAGTGTGATGGTCTTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGG;SVLEN=453;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	61919906	CPX_chr20:61919906-61920109	TCGTGATTATGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGCGGTGATTGCATGGAAGTGTGGTGTCACAGTGATTGCGTGGAAGCGTGTCGTGATTGTGTGGAAGCATGGTATCGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCATGTTGTGATTG	<CPX>	.	.	ALIGN_LENGTHS=947;ALT_ARRANGEMENT=1,2,3,UINS-177,1,2,2,3;CTG_GOOD_NONCANONICAL_MAPPING=chr20_KI270869v1_alt,32261,-,1273M69I860M17D47M6D52M4D37M6D50M6D42M6D76M3I47M6D25M3I102M3D79M76H,60,193,2065;CTG_NAMES=asm028707:tig00000;END=61920109;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=947;SEGMENTS=chr20:61919906-61919908,chr20:61919908-61920054,chr20:61920054-61920109;SEQ_ALT_HAPLOTYPE=TCGTGATTATGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGCGGTGATTGCATGGAAGTGTGGTGTCACAGTGATTGCGTGGAAGCGTGTCGTGATTGTGTGGAAGCATGGTATCGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTGTGATTGTGTGGAAGCATGGTATCGTGATTGTGGAAGCGTGGTATCGCGGCGATTGTGTGGAAGCGTGGTGTCGCAGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGTGTGGAAGCATGGTGTCGTGATTGTGTGGAAGCATGTCGTGATTGTGTGGAAGTGTGATGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGGAAGTGTGGTGTCACGCTGATTGCATGGAAGTGTGTTGTGATTGTGTGGAAGCGTGATATCGCAGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATCGGAAGCGTGGTGTTGCGGTGATTGCATGGAAGCATGTTGTGATTGTGTGGAAGCATGGTATCGTGATTGTCTGGAAGCATGGTGTCATGGTGATTGGAAGTGTGTCGTGATTG;SVLEN=204;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	62452038	CPX_chr20:62452038-62452236	GGGGAGAGAGGGAGGGTGAGAGTGGGGAGAGGGAGAGGGGAAGAAAGAGAGAAGGAGAGCGGGGAGAGAGAGGGAGAAGGGGGAGGAAGAGAGGGAGAAGGAGAGAGAGAAGGAGGGAGAGAGGGAGAGGGAGAGAAAGAGAAAGGGAAGGAGAGAGGGAGGGAAGGAAAGAGGGAGGGAGAGAAGGAAGCAGAGAGGG	<CPX>	.	.	ALIGN_LENGTHS=235;ALT_ARRANGEMENT=1,UINS-148,1,2;CTG_NAMES=asm028732:tig00001;END=62452236;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=235;SEGMENTS=chr20:62452038-62452041,chr20:62452041-62452087,chr20:62452087-62452236;SEQ_ALT_HAPLOTYPE=GGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGAGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGAGAGGGAGGGTGAGAGTGGGGAGAGGGAGAGGGGAAGAAAGAGAG;SVLEN=199;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	63092255	CPX_chr20:63092255-63094246	GGCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCTGCAGCACCCACATCCTGCCGACGCCATGCACGTGAGTGTGCATGTGGGGTGGGGGTGCGCCAGGAAGGCAAAAATCCCAAATGTCAGCGCCCGGTGATTTGAGGAGTTCAGACAAAGCCTTCCCTGGGGCTGTCCTCGGCCCACTTCCCCATCATCCCAATGTCCCTGCAGCCCTTGAAATGGCTCGGATGTGGGGCAGGAGGGCTGGGCGGATGCTGATCTGAGGCCGAGGTTGATGGATTCCGGCTCCCCCAGTGCCGATCCGGCTGCTGCCCCACGTGGGGCTTTGAGGCTGCGGCAACAGAGCCGGTGGGACACGCTCCTGATGCCAGACCCAGGGGTAAGAGCTGCCCCTGCTCCACGGTCTGCGCCACGATGGCTGCCAGAGCGAAAATGGGAGGGAGAGAAGCGCTGTCAGGGCCTCCCAGGGAGGGTGTGTGGCGTGTGGCTTGCTAAGCACCCTCTTTTCTGATCCCGCCCTGAGCAGCTCCCTGGGACTTTTGTTGGTCAAAGCTTCAGCTGTGGTCAGAGGATCCAACGCTGCCGTCAACAGGCAGCTGCTGCCGTATGGCTGCAGATGTGGTTTCTGGAACAGACGGGCCCAGCCCTGCAAGGTGGGCTGGCTCTTTGGCTCTCGAGAGCACCATGGCACAGTGCTGATCTGGGTCCACACGGCCCAGCCACCCGGTCAGCTCGCCTGGTTCTTACATTTCCACTCCACAAACAGAACCCAGACCCAGATCTGCTTCCTCCGCCTCCCGCCCTCCTCGCCCCGCACCGTTTCTTGTCCCACAGAAGCTGTCATGGGTGCTGTGTACCCCACAGGGCGGGAGAGAAAGGTGTGTCCAGGAGCAATCTCGGGAAACAGGGGGCAGAGGATGCGGTGCAGAGCCGAGCTCCGGAGCCACCTTCCTGACCGCCAGAGCCTGACTGCATCCGTATGGCATGAGGTCGGTATCTAGGAGGCCATACTCTTTACCTAACATCCAGGACACAGGAAAAGGACGGAAACAGAAAAAAATACATAAATAAATTCAAGATGCATTTTAAAGAACATGAAAAACTTTAAAAGGACGGGTAATTGTCTAACATTTTGTTAATTCAATCAGGCTTGCAATTTAAAAATAGCTTTGCCTTTTACTGAAAAAGAAATTAATTATAATTTCTTACTGAATCCAGGGAGAGAATTCGGGACTAGGGGGTTCCCTGAGAAGGTCTTCTTACACGTTACCCTCCAATGTCCTGTGGCCAAGGGAGCTTCAACCCCCTCTTTACGAGGGTTCTGGTGGCTGGAGAACTCAGAGACGGCTCTAAAAAAATTGCAAGCTGGCCAGGCACGGTGGCTCACCCCCGTATTCCCAGCACTTTAGGAGGCTGAGGCAGGCAGATCACCTGAGGTCAGGAGTTTGAGACCATCCTGGCCAACACGGTGAATCCCCGTCTCTACTAAAAATACAAAAATTAGCTGGACGTGGTGGCGCACGCCTGTAATCCCAGCTACTCAGGGGGCTGAGGCAGGAGAATCACTTGAACTTGGGAGGTGGAGGTCGCAGTGAGCCAAGATGGTGCCATTGCACCCCAGCCTGGGCGACAGAGCAAGACTTCATCTCAAAAAAATAAAAAAATGTAAACATCGCAAGCTGCACCCAGGTGTGAATCTGGAGGGCGCCTCCTTGGAAAACTTGGCTGGTGACCGCACCCTCAGTTCAAGCTCACCGGCCGCCCTTCCCTGTGCACACACGTGAGCTCTCCAGTATGTTTGGAATATCCCAGAGCCGCTGTCTCCTGGCTGCCCGGCCTCTGTGAGCCGCACTCCAGCCTGAAGGCCAAGACGGCTGCTCTGGAGAAAGAACTTCCCCTGGTGCTGAAGTCCCGAAGGAGAGCCCCATGGGCATGGGGAGGGGAGGGTGCCTCGCCCCCAAGGCTGCGCTGCTCCGCGGCC	<CPX>	.	.	ALIGN_LENGTHS=942;ALT_ARRANGEMENT=UINS-70,1;CTG_NAMES=asm028762:tig00002;END=63094246;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=942;SEGMENTS=chr20:63092256-63093346,chr20:63093346-63094246;SEQ_ALT_HAPLOTYPE=GGCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGATGCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGACGCCATGCACGTGAGTGTGCATGTGGGGCGGGGGTGCGCCAGGAAGGCAAAAATCCCAAATGTCAGCGCCCGGTGATTTGAGGAGTTCAGACAAAGCCTTCCCTGGGGCTGTCCTCGGCCCACTTCCCCATCATCCCAATGTCCCTGCAGCCCTTGAAATGGCTCGGATGTGGGGCAGGAGGGCTGGGCGGATGCTGATCTGAGGCCGAGGTTGATGGATTCCGGCTCCCCCAGTGCCGATCCGGCTGCTGCCCCACGTGGGGCTTTGAGGCTGCGGCAACAGAGCCGGTGGGACACGCTCCTGATGCCAGACCCAGGGGTAAGAGCTGCCCCTGCTCCACGGTCTGCGCCACGATGGCTGCCAGAGCGAAAATGGGAGGGAGAGAAGCGCTGTCAGGGCCTCCCAGGGAGGGTGTGTGGCGTGTGGCTTGCTAAGCACCCTCCTTTCTGATCCCGCCCTGAGCAGCTCCCTGGGACTTTTGTTGGTCAAAGCTTCAGCTGTGGTCAGAGGATCCAACGCTGCCGTCAACAGGCAGCTGCTGCCGTATGGCTGCAGACGTGGTTTCTGGAACAGACGGGCCCAGCCCTGCAAGGTGGGCTGGCTCTTTGGCTCTCGAGAGCACCACGGCACAGTGCTGATCTGGGTCCACACGGCCCAGCCACCCGGTCAGCTCGCCTGGTTCTTACATTTCCACTCCACAAACAGAACCCAGACCCAGATCTGCTTCCTCCGCCTCCCGCCCTCCTCGCCCCGCACCGTTTCTTGTCCCACAGAAGCTGTCATGGGTGCTGTGTACCCCATAGGGCGGGAGAGAAAGGTGTGTCCAGGAGCAATCTCGGGAAACAGGGGGCAGAGGATGCGGTGCAGAGCCGAGCTCCGGAGCCACCTTCCTGACCGCCAGAGCCTGACTGCATCCGTATGGCATGAGGTCGGTATCTAGGAGGCCATACTCTTTACCTAACATCCAGGACACAGGAAAAGGACGGAAACAGAAAAAAATACATAAATAAATTCAAGATGTC;SVLEN=1992;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	63353949	CPX_chr20:63353949-63354272	TCGGGGGGGCTGCGGTCCTGGGAGGTCTGTGGTCCTGGGGGGCTGTGGTCCTGGCGGGGGGGCTGCGGTCCTAGGGGTGTTGTAGTCCTAGGGGGCTGTGGTCAGGCAAGAACTGTGATCCTTGTGGGGGCTGCAGTTCTGCAGGAGGCACTGTAGCCCTAGGGTGGGATGAAGTCCTGGGAGGACTGTGGTCCTGGCAGGGAATGTGGTCCTGGGGGCCTGTGGTCCTGGGGGGCTGTGGTCCTGGGGGGGCTGTGGTCCTGGGGGGCTGTGGTCCTAGGGGGCTGTGGTCCTAAATGGGGCTGTGGTCCTGGGGGGCTGTAG	<CPX>	.	.	ALIGN_LENGTHS=81;ALT_ARRANGEMENT=2;CTG_NAMES=asm028777:tig00001;END=63354272;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=81;SEGMENTS=chr20:63353949-63354002,chr20:63354002-63354205,chr20:63354205-63354272;SEQ_ALT_HAPLOTYPE=TGGGGGGGAGCTGCTGTCCTAGGGGTGTTGTAGTCCTAGGGGGCTGTGGTCAGGCAAGAACTGTGATCCTTGTGGGGGCTGCAGTTCTGCAGGAGGCACTGTAGCCCTAGGGTGGGATGAAGTCCTGGGAGGACTGTGGTCCTGGCAGGGAATGTGGTCCTGGGGGCCTGTGGTCCTGGGGGGCTGTGGTCCTGGGGGAGCTGTGG;SVLEN=324;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr20	64096905	CPX_chr20:64096905-64097041	CCACCATCATCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACC	<CPX>	.	.	ALIGN_LENGTHS=166;ALT_ARRANGEMENT=1,1,UINS-166;CTG_NAMES=asm028821:tig00001;END=64097041;HQ_MAPPINGS=0;MAPPING_QUALITIES=54;MAX_ALIGN_LENGTH=166;SEGMENTS=chr20:64096905-64097041;SEQ_ALT_HAPLOTYPE=CCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACTGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGCCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAATCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACTATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATCATCACATTCATCATCACTATTACCATCATCATCACCACCATCACCATCACTATCACCACCATCATTACATTTGTCACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACCGTC;SVLEN=137;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr21	21264944	CPX_chr21:21264944-21265096	TATATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTCTGTGTATATATGTACACATATATACTATATATGTGTATGTGTATATATATACACACATATATTATATAT	<CPX>	.	.	ALIGN_LENGTHS=316,316;ALT_ARRANGEMENT=1,2,3,2,1,2,3;CTG_NAMES=asm029034:tig00000,asm029034:tig00001;END=21265096;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=316;SEGMENTS=chr21:21264944-21264988,chr21:21264988-21265052,chr21:21265052-21265096;SEQ_ALT_HAPLOTYPE=TATATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATATGTATATATACACATATATATTATATATATATGTGTCTGTATATATATACACATATATATTATATATATGTGTCTGTGTATATATATACACATATATATGTGTCTGTGTATATATGTACACATATATACTATATATGTGTATGTGTATATATATACACACATATATTATATAT;SVLEN=153;SVTYPE=CPX;TOTAL_MAPPINGS=2
-chr21	23428920	CPX_chr21:23428920-23429023	TTTATATAAATATATATAAATATATAATATATAATAATATAATATAATATATATATAATATAATATAATATAATATATAATATATATTACATAATATATTATAT	<CPX>	.	.	ALIGN_LENGTHS=1182,1182;ALT_ARRANGEMENT=UINS-84,2,3,UINS-5,2,2,3;CTG_NAMES=asm029052:tig00000,asm029052:tig00001;END=23429023;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1182;SEGMENTS=chr21:23428920-23428968,chr21:23428968-23428998,chr21:23428998-23429023;SEQ_ALT_HAPLOTYPE=TATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATAATATATATAATATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATAT;SVLEN=104;SVTYPE=CPX;TOTAL_MAPPINGS=2
-chr21	26001843	CPX_chr21:26001843-26002386	ATCACATCTAGGCATGGCTTTGAGCTTCACAGGCCAGAAGCTGCTCTGTCAGTAACTCAGAGGGGATATGGTCCCTAGACCCAATTCACTTTTAATAAATCAGGGTGCCAGTCCTTTAATTTTGGAAGATAAATAAAATTGCGAAGTAGATGGGATACTTACGTCAACAAGTTGGTTGGGTTTCATCCTGTAAGAGTATTGTGTACAGAAATCCAATTTGCTTTGGGAGCGTGGACTTTGAAAGCAGCAGTACTGAGTGAGATGGCCTTAATGATGGATGATAATGAGGTTGATGCTTTCGTAGCCACGTTTCCATCTGAAAACCACGTGAAGAGTGTCAGATCATCTTCATGTCCGTTGCATGGCGCATTTCTCCTGCGGAGTGTTTGACACCTTCTGGGCTTAGTGCTGACTGTCCCTCCTGTTGACATCATCGTGATGGTAGCCACCTCTGGTTTTACCAGTACTTTATTGCATCTACTGAAAGAGCAACGTGTATAGGGAAGTAAAACAATAGTTAGTCCCCATTTGTATTGACATTGTG	<CPX>	.	.	ALIGN_LENGTHS=1370;ALT_ARRANGEMENT=-1;CTG_NAMES=asm029075:tig00000;END=26002386;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1370;SEGMENTS=chr21:26001844-26002384,chr21:26002384-26002386;SEQ_ALT_HAPLOTYPE=ACAATGTCAATACAAATGGGGACTAACTATTGTTTTACTTCCCTATACACGTTGCTCTTTCAGTAGATGCAATAAAGTACTGGTAAAACCAGAGGTGGCTACCATCACGATGATGTCAACAGGAGGGACAGTCAGCACTAAGCCCAGAAGGTGTCAAACACTCCGCAGGAGAAATGCGCCATGCAACGGACATGAAGATGATCTGACACTCTTCACGTGGTTTTCAGATGGAAACGTGGCTACGAAAGCATCAACCTCATTATCATCCATCATTAAGGCCATCTCACTCAGTACTGCTGCTTTCAAAGTCCACGCTCCCAAAGCAAATTGGATTTCTGTACACAATACTCTTACAGGATGAAACCCAACCAACTTGTTGACGTAAGTATCCCATCTACTTCGCAATTTTATTTATCTTCCAAAATTAAAGGACTGGCACCCTGATTTATTAAAAGTGAATTGGTTCTAGGGACCATATCCCCTCTGAGTTACTGACAGAGCAGCTTCTGGCCTGTGAAGCTCAAAGCCATGCCTAGATGTGAG;SVLEN=544;SVTYPE=CPX;TOTAL_MAPPINGS=1
-chr21	46069065	CPX_chr21:46069065-46069209	CACACGTGTGTGCATGTGTGTGCATGTGTGCCTGGGTGTGTGTGCACGCCTGTGTGAGCATGTGTGCCTGAATGTGTGTGCATGTGTGTGCAAGTTCATGTGTGTGCCTGTGTGCATGTGTGCCTGTGTGTACGTGTGTGTGCCA	<CPX>	.	.	ALIGN_LENGTHS=154,154;ALT_ARRANGEMENT=UINS-59,1;CTG_NAMES=asm029362:tig00001,asm029362:tig00002;END=46069209;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=154;SEGMENTS=chr21:46069066-46069156,chr21:46069156-46069209;SEQ_ALT_HAPLOTYPE=CCTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGTGCATGTGTGCCTGGGTGTGTGTGCACGCCTGTGTGAGCATGTGTGCCTGGATGTGTGTGCATGTGTGTGCAA;SVLEN=145;SVTYPE=CPX;TOTAL_MAPPINGS=2
+chr20	2379056	CPX_chr20:2379056-2379968	C	<CPX>	.	.	ALIGN_LENGTHS=1401;ALT_ARRANGEMENT=1,2,3,UINS-4,1,3;CTG_NAMES=asm027854:tig00003;END=2379968;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1401;SEGMENTS=chr20:2379056-2379257,chr20:2379257-2379963,chr20:2379963-2379968;SEQ_ALT_HAPLOTYPE=CTGCTGAAGGTCACACAGCCAGTTTGGCCCAGAGATAACAGAACCCAGGACTCTACTGCCAGGCTATGATGCTCACTTCTAAACTGAGTATGGGCCGGGTGCAGTGGCTCTCACTTGGAATCTCGCACTTTGGGAGGCTGAGGTGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACTGTCTCTACTTAAAATACACAAAAAATTAGCCGGGCATGGTGGCACACGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAAGTAGAGGTTGCACCGAGCTGAGATCGTGCCGCTGCACTTCACCCTAGGTGACAGAGCGAGACCCTGTCTCAAAAAAAAAAAACGAGGAGTATGAATTATTATTTGGGGTCTCGAGCAGTGGGGCAGGCAGTGATTTTGATGCCCTGTCTTCTGGGAGCTCCCGTCCAAGCAAGCCCAGGATGAAAGATAAAAGGGCCCTGAATAAGACCATCATTAGTGGGGAGGAGCCTGACCCTGCATAGGCAGAAAAGCAGCTTCAGCAGGGCCCAGGGTCTACAGGGCAGCAGCCTGCAGGGTGTTGAGGAAGGAGCTGCCCTGGGCTGCTGCCAGATGTCAGTAATTATAAGGCTATGTGGGTCTGCAGACAGCTCATTAAAGACGCTTGATCTGCGTGAAACCAGGAAGCAGAACTCAGCCTCTTTGCCACTTTCTGTAAGAAATCCAACCACATCAAACACTTTGGGGTTTTTATGCAGTTTCCTGAATGTTGGGGTGATCCCAGGGAGCGGCCTCATCCTACTGTGCTCAGCACACGGTTGTCTCCTTACCCTTCCTTGTCTCTTTCCCTCGATTCTACCCCCTCCCACTTCCCCTTCCTCACTGGCCCAGTGAGGCTGCTGAAGGTCACACAGCCAGTTTGGCCCAGAGATAACAGAACCCAGGACTCTACTGCCAGGCTATGATGCTCACTTCTAAACTGAGTATGGGCCGGGTGCAGTGGCTCTCACTTGTAATCTCGCACTTTGGGAGGCTGAGGTGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACTGTGCCCAG;SVLEN=913;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	12558793	CPX_chr20:12558793-12558810	A	<CPX>	.	.	ALIGN_LENGTHS=597;ALT_ARRANGEMENT=-chrX:99014092-99014129,UINS-101;CTG_NAMES=asm027960:tig00003;END=12558810;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=597;SEGMENTS=chr20:12558793-12558810;SEQ_ALT_HAPLOTYPE=AGACAAAGAAACAAACAAACAAAACAAAACTATATATATATATATATACACACACACACACACACACACATTATTAAAATTCAGATTTAAATAAACTGACTATAAAAAAGTACTTTTGAAACAAAAACTTTAATCATGATTATATATATTA;SVLEN=18;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	18675721	CPX_chr20:18675721-18675877	T	<CPX>	.	.	ALIGN_LENGTHS=564;ALT_ARRANGEMENT=1,UINS-28,1,UINS-64,1;CTG_NAMES=asm028012:tig00004;END=18675877;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=564;SEGMENTS=chr20:18675721-18675877;SEQ_ALT_HAPLOTYPE=TATGTGTATATTTACACACATATATATGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCGATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTAAATATACCTATGTGT;SVLEN=157;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	20269131	CPX_chr20:20269131-20269199	A	<CPX>	.	.	ALIGN_LENGTHS=40;ALT_ARRANGEMENT=-chrX:137700299-137700331;CTG_NAMES=asm028026:tig00000;END=20269199;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=40;SEGMENTS=chr20:20269131-20269199;SEQ_ALT_HAPLOTYPE=ACACACACACACACACACACACACACACACACACA;SVLEN=69;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	23122561	CPX_chr20:23122561-23122996	C	<CPX>	.	.	ALIGN_LENGTHS=876,876;ALT_ARRANGEMENT=1,2,-1;CTG_NAMES=asm028059:tig00000,asm028059:tig00001;END=23122996;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=876;SEGMENTS=chr20:23122561-23122596,chr20:23122596-23122666,chr20:23122666-23122996;SEQ_ALT_HAPLOTYPE=CTGTCATGTCACCGTGTGGGAGGGCTTGCAGGTGAAGTGGTCTGGGAGGGGTCCCCCAGACAAAGCCAAGGTTCTGAGAGTTGGCCCGAACACTGCTGGATTCCACTTCACCTGCAAGCCCTCCCACACGGTGACATGACAGC;SVLEN=436;SVTYPE=CPX;TOTAL_MAPPINGS=2
+chr20	28561412	CPX_chr20:28561412-28561576	A	<CPX>	.	.	ALIGN_LENGTHS=416;ALT_ARRANGEMENT=UINS-74,1,UINS-74;CTG_NAMES=asm008294:tig00014;END=28561576;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=416;SEGMENTS=chr20:28561413-28561575;SEQ_ALT_HAPLOTYPE=AACATCATATGTGACAGGCTCTCATAGTCACCATCATCACAGAAATCTCGCGCATGTTACAGAGAAGCACTGTCCTACATCATATGTGACAGGCTCTCATAGTCACCATTCCCATGACCATAGTCATGGGAATCTTGCTCATGTTACAGGGAAGCACTGTCCAACATCATATGTGACAGGCTCTCATCGTCACCATCATCATGGGAATCTTGTGCATGTTACAGGGAAGCATTGTCCTACATCGTATGTGACAGGCTCTCATAATCACTATCATCATGGGAATCCTGTGCATGTTACAGGAAAGAACTGTCCTGC;SVLEN=165;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	38123803	CPX_chr20:38123803-38124181	A	<CPX>	.	.	ALIGN_LENGTHS=1516,1516;ALT_ARRANGEMENT=1,2,3,UINS-5,1,UINS-531,3,4,3,4;CTG_NAMES=asm028411:tig00000,asm028411:tig00001;END=38124181;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1516;SEGMENTS=chr20:38123803-38123868,chr20:38123868-38124004,chr20:38124004-38124014,chr20:38124014-38124181;SEQ_ALT_HAPLOTYPE=ATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATA;SVLEN=379;SVTYPE=CPX;TOTAL_MAPPINGS=2
+chr20	38653054	CPX_chr20:38653054-38653283	T	<CPX>	.	.	ALIGN_LENGTHS=1534;ALT_ARRANGEMENT=1,2,3,4,3,1,2,3,4,5,2,3,4,5;CTG_NAMES=asm028418:tig00000;END=38653283;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1534;SEGMENTS=chr20:38653054-38653113,chr20:38653113-38653145,chr20:38653145-38653179,chr20:38653179-38653273,chr20:38653273-38653283;SEQ_ALT_HAPLOTYPE=TGGTGGTGGTGGTGATGGAAATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGATGGTGGTGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGGTGATAATGATGGTAGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGGTGATGGAAATGATGATGATGTTAATTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGATGGTGATGATGATTATGATGGTGGTGGTGGTGGTGGTGGTGCTGGTGATAGTGGTGGTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGGTGTTGGTGGTGCTGGTGATGATAATCATGCTGGTGGTGGTGGCGTTGATGATGGTGACAGTAGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTGGTGATGATGGTGATG;SVLEN=230;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	47895195	CPX_chr20:47895195-47895581	A	<CPX>	.	.	ALIGN_LENGTHS=289;ALT_ARRANGEMENT=2;CTG_NAMES=asm028508:tig00005;END=47895581;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=289;SEGMENTS=chr20:47895195-47895294,chr20:47895294-47895482,chr20:47895482-47895581;SEQ_ALT_HAPLOTYPE=AAGGGTCCGGAAGCTGGTGACCCAGGGAGGAGAGGTCTTGATCTGGTCTGAGGGTCGTGGAGCTACAGACCCAGGGAGGAGCAATGTTGTTGTAGTTCGAGGGTCCGGTAGCTGGCAACCCGGGAAAGAGAAGTCTTGTTCGAGTTTGAGGGTCGTGGAGCTGCAGACCCAGGGAGGAGCAATTTTGTTGT;SVLEN=387;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	51740560	CPX_chr20:51740560-51740561	A	<CPX>	.	.	ALIGN_LENGTHS=1104,1104;ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496;CTG_NAMES=asm028558:tig00002,asm028558:tig00003;END=51740561;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1104;SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGT;SVLEN=2;SVTYPE=CPX;TOTAL_MAPPINGS=2
+chr20	51740560	CPX_chr20:51740560-51741035	A	<CPX>	.	.	ALIGN_LENGTHS=895,895;ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496,1,UINS-49;CTG_NAMES=asm028558:tig00000,asm028558:tig00001;END=51741035;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=895;SEGMENTS=chr20:51740561-51741034;SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGTTTTGTGTTGTTGTTTTTGTTTTTTGAGACAAGGTCTCATTCTGTCACCCAGGCAGGACTGTGGTGGCACCATCATGGCTCAGCGCAGCCTCCTTTTCCCCAGGCTCAAGTGATCCTCTTGCCTCAGCCTCCCACGTGGCTGGGACTACAGGTGTGTACCACCACTCCCGGATAATTTTTTTTATTTTTTATTTTTAGTAAAGACAGTCTCACTATGTTGCCCAGGCTGGTCTCCAACTCCTGGTCTCAAGCAATCCTCCCAGTTCAGCCTCTCAAAGTGCTGGGATTACAGATGTGAGCCACAATACCCGGCCCCAATTCTAATGTTTAAAGAGTACAGTCTACACCTTAAAGCCTGCATTTTATCATCCTGTCCTCACTGCTCTGACTTCTTTACAGTTGTGCTGTCCACCTTGGCGGCTTCTACCACATGTGGCTATTTTAAGTTTCAATTAATTAAAATTAAATTTTAATTTAATTAATTAAAAATAAATTTTAATTAATTAATTAAAAATAAATTTTAAT;SVLEN=476;SVTYPE=CPX;TOTAL_MAPPINGS=2
+chr20	54849491	CPX_chr20:54849491-54849615	C	<CPX>	.	.	ALIGN_LENGTHS=88;ALT_ARRANGEMENT=UINS-36,-chr14:58474127-58474172,UINS-54;CTG_NAMES=asm028586:tig00000;END=54849615;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=88;SEGMENTS=chr20:54849491-54849615;SEQ_ALT_HAPLOTYPE=CCAAATCTCATGTTGAAATGTAATCCCCAGTGTTGGAGGGGGGCAGATCCCTCATGAATGGCTTGGTGCCCTTCCCATGGTAATGAGTGAGTTCTTGCTCTGTTAGTTCATGAGAGAGCTGATTGTTTAAAGGAGTCTGG;SVLEN=125;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	58695019	CPX_chr20:58695019-58695020	G	<CPX>	.	.	ALIGN_LENGTHS=82;ALT_ARRANGEMENT=UINS-72,chr20:58695237-58695339,UINS-83,chr20:58695287-58695340,UINS-12,chr20:58695229-58695328,UINS-27,chr20:58695237-58695320;CTG_NAMES=asm028638:tig00002;END=58695020;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=82;SEQ_ALT_HAPLOTYPE=TTGCGTGTGTATGAGTGCTGGTGTGTGCATGAATGGTGTGTGTGGTGTGTTTATGTGTGGTGTGTGTTGCTGTGTGAGTGCTGGTGTGTGCATGAGTGGCGTGTGTGTGGTGTGTGTTGCTGTGTGTGTATGAGTGTTGGTGTGTGCATGAGTGGTGTGTGTGTGCTGTGTGTATGTGTGGTGTGTGTTGCTGTGTATGAGTGTTGGTGTGTGCATGAGTGGTGTGTGTGTGCTGTGTGTACGTGTGTGTGTTGCTGTGTGTGTGTTTGAGTGCTGGTGTGTGCATGAGTGGTGTGTGTGTGGTGTGTGTGGTGTCTGTTGCTGTGTGTGTTTGAGTTCTGGTATGTGCATGAGTGGTGTGTGTGTGTGCTGTGTGTGTGGTGTGTTGCTGTGTGTGTATGAGTGCTGGTGTGTGCACGAGTGGTGTGTGTATTTGCGGTGTGTGTTGCTGTGTATATGTGAGTGCTGGTGTGTGCATGAGTGGCGTGTGTGGTGTGTATGTGTGGTGTGTGTTGCTGTTTGTGTTTGAGTGCTGATGTGTGCATGAGTGG;SVLEN=2;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	61375650	CPX_chr20:61375650-61376102	T	<CPX>	.	.	ALIGN_LENGTHS=1559;ALT_ARRANGEMENT=1,2,3,2,1,2,3;CTG_NAMES=asm028687:tig00001;END=61376102;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1559;SEGMENTS=chr20:61375650-61375759,chr20:61375759-61375874,chr20:61375874-61376102;SEQ_ALT_HAPLOTYPE=TGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTAGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGCTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGCTCTTGGTGCTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGATGATAGTGGGGTTTATTGATGGTAGTGTGATGGTCTTGGTGGTGCTGATAATGGTGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTGGCGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGGTGATGATGTAGTTTGTTGATGGTAGCGTGATGTTCTTGGTGCTGGTGGTGGTGATGATGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGGTGGTGGTGATAGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGATGCTGGTGATGGTATTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTCGTGGTGGTGGTGTGGTTTGTCGATGGTAGTGTGGTGGTCTTGGTGCTGGTGGTTGTCGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGATGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTAGTGATGGTGTGGTTTGCTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATACTGTGGTTTGTGGATGGTAGTGTGATGGTCTTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGG;SVLEN=453;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	61919906	CPX_chr20:61919906-61920109	T	<CPX>	.	.	ALIGN_LENGTHS=947;ALT_ARRANGEMENT=1,2,3,UINS-177,1,2,2,3;CTG_GOOD_NONCANONICAL_MAPPING=chr20_KI270869v1_alt,32261,-,1273M69I860M17D47M6D52M4D37M6D50M6D42M6D76M3I47M6D25M3I102M3D79M76H,60,193,2065;CTG_NAMES=asm028707:tig00000;END=61920109;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=947;SEGMENTS=chr20:61919906-61919908,chr20:61919908-61920054,chr20:61920054-61920109;SEQ_ALT_HAPLOTYPE=TCGTGATTATGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGCGGTGATTGCATGGAAGTGTGGTGTCACAGTGATTGCGTGGAAGCGTGTCGTGATTGTGTGGAAGCATGGTATCGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTGTGATTGTGTGGAAGCATGGTATCGTGATTGTGGAAGCGTGGTATCGCGGCGATTGTGTGGAAGCGTGGTGTCGCAGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGTGTGGAAGCATGGTGTCGTGATTGTGTGGAAGCATGTCGTGATTGTGTGGAAGTGTGATGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGGAAGTGTGGTGTCACGCTGATTGCATGGAAGTGTGTTGTGATTGTGTGGAAGCGTGATATCGCAGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATCGGAAGCGTGGTGTTGCGGTGATTGCATGGAAGCATGTTGTGATTGTGTGGAAGCATGGTATCGTGATTGTCTGGAAGCATGGTGTCATGGTGATTGGAAGTGTGTCGTGATTG;SVLEN=204;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	62452038	CPX_chr20:62452038-62452236	G	<CPX>	.	.	ALIGN_LENGTHS=235;ALT_ARRANGEMENT=1,UINS-148,1,2;CTG_NAMES=asm028732:tig00001;END=62452236;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=235;SEGMENTS=chr20:62452038-62452041,chr20:62452041-62452087,chr20:62452087-62452236;SEQ_ALT_HAPLOTYPE=GGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGAGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGAGAGGGAGGGTGAGAGTGGGGAGAGGGAGAGGGGAAGAAAGAGAG;SVLEN=199;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	63092255	CPX_chr20:63092255-63094246	G	<CPX>	.	.	ALIGN_LENGTHS=942;ALT_ARRANGEMENT=UINS-70,1;CTG_NAMES=asm028762:tig00002;END=63094246;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=942;SEGMENTS=chr20:63092256-63093346,chr20:63093346-63094246;SEQ_ALT_HAPLOTYPE=GGCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGATGCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGACGCCATGCACGTGAGTGTGCATGTGGGGCGGGGGTGCGCCAGGAAGGCAAAAATCCCAAATGTCAGCGCCCGGTGATTTGAGGAGTTCAGACAAAGCCTTCCCTGGGGCTGTCCTCGGCCCACTTCCCCATCATCCCAATGTCCCTGCAGCCCTTGAAATGGCTCGGATGTGGGGCAGGAGGGCTGGGCGGATGCTGATCTGAGGCCGAGGTTGATGGATTCCGGCTCCCCCAGTGCCGATCCGGCTGCTGCCCCACGTGGGGCTTTGAGGCTGCGGCAACAGAGCCGGTGGGACACGCTCCTGATGCCAGACCCAGGGGTAAGAGCTGCCCCTGCTCCACGGTCTGCGCCACGATGGCTGCCAGAGCGAAAATGGGAGGGAGAGAAGCGCTGTCAGGGCCTCCCAGGGAGGGTGTGTGGCGTGTGGCTTGCTAAGCACCCTCCTTTCTGATCCCGCCCTGAGCAGCTCCCTGGGACTTTTGTTGGTCAAAGCTTCAGCTGTGGTCAGAGGATCCAACGCTGCCGTCAACAGGCAGCTGCTGCCGTATGGCTGCAGACGTGGTTTCTGGAACAGACGGGCCCAGCCCTGCAAGGTGGGCTGGCTCTTTGGCTCTCGAGAGCACCACGGCACAGTGCTGATCTGGGTCCACACGGCCCAGCCACCCGGTCAGCTCGCCTGGTTCTTACATTTCCACTCCACAAACAGAACCCAGACCCAGATCTGCTTCCTCCGCCTCCCGCCCTCCTCGCCCCGCACCGTTTCTTGTCCCACAGAAGCTGTCATGGGTGCTGTGTACCCCATAGGGCGGGAGAGAAAGGTGTGTCCAGGAGCAATCTCGGGAAACAGGGGGCAGAGGATGCGGTGCAGAGCCGAGCTCCGGAGCCACCTTCCTGACCGCCAGAGCCTGACTGCATCCGTATGGCATGAGGTCGGTATCTAGGAGGCCATACTCTTTACCTAACATCCAGGACACAGGAAAAGGACGGAAACAGAAAAAAATACATAAATAAATTCAAGATGTC;SVLEN=1992;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	63353949	CPX_chr20:63353949-63354272	T	<CPX>	.	.	ALIGN_LENGTHS=81;ALT_ARRANGEMENT=2;CTG_NAMES=asm028777:tig00001;END=63354272;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=81;SEGMENTS=chr20:63353949-63354002,chr20:63354002-63354205,chr20:63354205-63354272;SEQ_ALT_HAPLOTYPE=TGGGGGGGAGCTGCTGTCCTAGGGGTGTTGTAGTCCTAGGGGGCTGTGGTCAGGCAAGAACTGTGATCCTTGTGGGGGCTGCAGTTCTGCAGGAGGCACTGTAGCCCTAGGGTGGGATGAAGTCCTGGGAGGACTGTGGTCCTGGCAGGGAATGTGGTCCTGGGGGCCTGTGGTCCTGGGGGGCTGTGGTCCTGGGGGAGCTGTGG;SVLEN=324;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr20	64096905	CPX_chr20:64096905-64097041	C	<CPX>	.	.	ALIGN_LENGTHS=166;ALT_ARRANGEMENT=1,1,UINS-166;CTG_NAMES=asm028821:tig00001;END=64097041;HQ_MAPPINGS=0;MAPPING_QUALITIES=54;MAX_ALIGN_LENGTH=166;SEGMENTS=chr20:64096905-64097041;SEQ_ALT_HAPLOTYPE=CCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACTGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGCCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAATCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACTATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATCATCACATTCATCATCACTATTACCATCATCATCACCACCATCACCATCACTATCACCACCATCATTACATTTGTCACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACCGTC;SVLEN=137;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr21	21264944	CPX_chr21:21264944-21265096	T	<CPX>	.	.	ALIGN_LENGTHS=316,316;ALT_ARRANGEMENT=1,2,3,2,1,2,3;CTG_NAMES=asm029034:tig00000,asm029034:tig00001;END=21265096;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=316;SEGMENTS=chr21:21264944-21264988,chr21:21264988-21265052,chr21:21265052-21265096;SEQ_ALT_HAPLOTYPE=TATATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATATGTATATATACACATATATATTATATATATATGTGTCTGTATATATATACACATATATATTATATATATGTGTCTGTGTATATATATACACATATATATGTGTCTGTGTATATATGTACACATATATACTATATATGTGTATGTGTATATATATACACACATATATTATATAT;SVLEN=153;SVTYPE=CPX;TOTAL_MAPPINGS=2
+chr21	23428920	CPX_chr21:23428920-23429023	T	<CPX>	.	.	ALIGN_LENGTHS=1182,1182;ALT_ARRANGEMENT=UINS-84,2,3,UINS-5,2,2,3;CTG_NAMES=asm029052:tig00000,asm029052:tig00001;END=23429023;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1182;SEGMENTS=chr21:23428920-23428968,chr21:23428968-23428998,chr21:23428998-23429023;SEQ_ALT_HAPLOTYPE=TATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATAATATATATAATATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATAT;SVLEN=104;SVTYPE=CPX;TOTAL_MAPPINGS=2
+chr21	26001843	CPX_chr21:26001843-26002386	A	<CPX>	.	.	ALIGN_LENGTHS=1370;ALT_ARRANGEMENT=-1;CTG_NAMES=asm029075:tig00000;END=26002386;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1370;SEGMENTS=chr21:26001844-26002384,chr21:26002384-26002386;SEQ_ALT_HAPLOTYPE=ACAATGTCAATACAAATGGGGACTAACTATTGTTTTACTTCCCTATACACGTTGCTCTTTCAGTAGATGCAATAAAGTACTGGTAAAACCAGAGGTGGCTACCATCACGATGATGTCAACAGGAGGGACAGTCAGCACTAAGCCCAGAAGGTGTCAAACACTCCGCAGGAGAAATGCGCCATGCAACGGACATGAAGATGATCTGACACTCTTCACGTGGTTTTCAGATGGAAACGTGGCTACGAAAGCATCAACCTCATTATCATCCATCATTAAGGCCATCTCACTCAGTACTGCTGCTTTCAAAGTCCACGCTCCCAAAGCAAATTGGATTTCTGTACACAATACTCTTACAGGATGAAACCCAACCAACTTGTTGACGTAAGTATCCCATCTACTTCGCAATTTTATTTATCTTCCAAAATTAAAGGACTGGCACCCTGATTTATTAAAAGTGAATTGGTTCTAGGGACCATATCCCCTCTGAGTTACTGACAGAGCAGCTTCTGGCCTGTGAAGCTCAAAGCCATGCCTAGATGTGAG;SVLEN=544;SVTYPE=CPX;TOTAL_MAPPINGS=1
+chr21	46069065	CPX_chr21:46069065-46069209	C	<CPX>	.	.	ALIGN_LENGTHS=154,154;ALT_ARRANGEMENT=UINS-59,1;CTG_NAMES=asm029362:tig00001,asm029362:tig00002;END=46069209;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=154;SEGMENTS=chr21:46069066-46069156,chr21:46069156-46069209;SEQ_ALT_HAPLOTYPE=CCTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGTGCATGTGTGCCTGGGTGTGTGTGCACGCCTGTGTGAGCATGTGTGCCTGGATGTGTGTGCATGTGTGTGCAA;SVLEN=145;SVTYPE=CPX;TOTAL_MAPPINGS=2