diff --git a/src/main/java/picard/sam/AbstractAlignmentMerger.java b/src/main/java/picard/sam/AbstractAlignmentMerger.java
index e7a5390df..6b4e0ac43 100644
--- a/src/main/java/picard/sam/AbstractAlignmentMerger.java
+++ b/src/main/java/picard/sam/AbstractAlignmentMerger.java
@@ -632,6 +632,7 @@ private void transferAlignmentInfoToFragment(final SAMRecord unaligned, final SA
                 unaligned.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
                 unaligned.setCigar(null);
                 unaligned.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);
+                unaligned.setAttribute(SAMTag.NM.name(), null);
             }
 
             unaligned.setReadUnmappedFlag(true);
@@ -659,7 +660,14 @@ static private String encodeMappingInformation(SAMRecord rec) {
                 ((Integer) rec.getAlignmentStart()).toString(),
                 rec.getCigarString(),
                 ((Integer) rec.getMappingQuality()).toString(),
-                rec.getStringAttribute(SAMTag.NM.name()))+";";
+                getStringOfNullable(rec.getIntegerAttribute(SAMTag.NM.name()))) + ";";
+    }
+
+    //returns the toString() of its input or an empty string if null.
+    static private String getStringOfNullable(final Object obj) {
+        return Optional.ofNullable(obj)
+                .map(Object::toString)
+                .orElse("");
     }
 
     /**
diff --git a/src/test/java/picard/sam/MergeBamAlignmentTest.java b/src/test/java/picard/sam/MergeBamAlignmentTest.java
index 2230923ec..5c08ad9c4 100644
--- a/src/test/java/picard/sam/MergeBamAlignmentTest.java
+++ b/src/test/java/picard/sam/MergeBamAlignmentTest.java
@@ -1697,7 +1697,7 @@ private MostDistantStrategyAlignmentSpec(final boolean expectedPrimary, final St
     public Object[][]  UnmappedReadStrategiesProvider() {
         return new Object[][] {
                 {AbstractAlignmentMerger.UnmappingReadStrategy.DO_NOT_CHANGE, "contam.expected.NO_CHANGE.sam"},
-                {null,                                                          "contam.expected.NO_CHANGE.sam"},
+                {null,                                                        "contam.expected.NO_CHANGE.sam"},
                 {AbstractAlignmentMerger.UnmappingReadStrategy.COPY_TO_TAG,   "contam.expected.COPY_TO_TAG.sam"},
                 {AbstractAlignmentMerger.UnmappingReadStrategy.MOVE_TO_TAG,   "contam.expected.MOVE_TO_TAG.sam"}
         };
@@ -1717,7 +1717,7 @@ public void testContaminationDetection(final AbstractAlignmentMerger.UnmappingRe
                 false, true, false, 1,
                 "0", "1.0", "align!", "myAligner",
                 true, refFasta, mergedSam,
-                null, null, null, null, true, null, strategy);
+                null, null, null, null, true, SAMFileHeader.SortOrder.coordinate, strategy);
 
         assertSamValid(mergedSam);
         IOUtil.assertFilesEqual(expectedSam, mergedSam);
diff --git a/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam b/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam
index 1d0144849..8bde03203 100644
--- a/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam
+++ b/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam
@@ -8,17 +8,17 @@
 @CO	r1_clipped_r2_clipped should be marked contaminant because at least one segment is overclipped
 @CO	r1_clipped_r2_perfect should be marked contaminant because at least one segment is overclipped
 @CO	r1_clipped_r2_unmapped should be marked contaminant because at least one segment is overclipped
-frag_multiple_primary_1	0	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
-frag_multiple_primary_1	0	chr1	1	15	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
-frag_multiple_primary_2	0	chr1	1	15	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
-frag_multiple_primary_2	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
-frag_primary_clipped	0	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
+frag_multiple_primary_1	0	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0	NM:i:0
+frag_multiple_primary_1	0	chr1	1	15	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0	NM:i:1
+frag_multiple_primary_2	0	chr1	1	15	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0	NM:i:10
+frag_multiple_primary_2	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0	NM:i:35
+frag_primary_clipped	0	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0	NM:i:0
 frag_primary_clipped	256	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
 frag_primary_clipped	2048	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
 frag_secondary_clipped	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
 frag_secondary_clipped	256	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
 r1_clipped_r2_clipped	97	chr1	1	30	20S10M20S	chr1	51	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
-r1_clipped_r2_clipped	145	chr1	51	30	20S10M20S	chr1	1	0	TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA	??????????????????????????????????????????????????	RG:Z:0
+r1_clipped_r2_clipped	145	chr1	51	30	20S10M20S	chr1	1	0	TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA	??????????????????????????????????????????????????	RG:Z:0	NM:i:37
 r1_clipped_r2_perfect	97	chr1	1	30	20S10M20S	chr1	51	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
 r1_clipped_r2_perfect	145	chr1	51	30	50M	chr1	1	0	TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA	??????????????????????????????????????????????????	RG:Z:0
 r1_clipped_r2_unmapped	73	chr1	1	30	20S10M20S	chr1	51	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	RG:Z:0
diff --git a/testdata/picard/sam/MergeBamAlignment/contam.expected.COPY_TO_TAG.sam b/testdata/picard/sam/MergeBamAlignment/contam.expected.COPY_TO_TAG.sam
index 4dca588a6..6b47b2699 100644
--- a/testdata/picard/sam/MergeBamAlignment/contam.expected.COPY_TO_TAG.sam
+++ b/testdata/picard/sam/MergeBamAlignment/contam.expected.COPY_TO_TAG.sam
@@ -2,15 +2,15 @@
 @SQ	SN:chr1	LN:1000	M5:17522ddd273279f4595f50fea9864734	UR:file:testdata/net/sf/picard/sam/MergeBamAlignment/cliptest.fasta
 @RG	ID:0	SM:Hi,Mom!	PL:ILLUMINA
 @PG	ID:0	VN:1.0	CL:align!	PN:myAligner
-frag_multiple_primary_1	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+frag_multiple_primary_1	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,0;	PG:Z:0	RG:Z:0	NM:i:0	CO:Z:Cross-species contamination
 frag_multiple_primary_2	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:50	PG:Z:0	RG:Z:0	NM:i:0	UQ:i:0
 frag_multiple_primary_2	256	chr1	1	15	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:0T0T0C0A0T1C0T0G1	PG:Z:0	RG:Z:0	NM:i:8	UQ:i:240
-frag_primary_clipped	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+frag_primary_clipped	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,0;	PG:Z:0	RG:Z:0	NM:i:0	CO:Z:Cross-species contamination
 frag_secondary_clipped	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:50	PG:Z:0	RG:Z:0	NM:i:0	UQ:i:0
 frag_secondary_clipped	256	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:0T0T0C0A0T1C0T0G1	PG:Z:0	RG:Z:0	NM:i:8	UQ:i:240
-r1_clipped_r2_clipped	109	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-r1_clipped_r2_perfect	109	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-r1_clipped_r2_unmapped	77	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_clipped	109	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_perfect	109	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_unmapped	77	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
 r1_clipped_r2_unmapped	141	*	0	0	*	*	0	0	TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0
-r1_clipped_r2_clipped	157	*	0	0	20S10M20S	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-r1_clipped_r2_perfect	157	*	0	0	50M	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,50M,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_clipped	157	*	0	0	20S10M20S	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,20S10M20S,30,37;	PG:Z:0	RG:Z:0	NM:i:37	CO:Z:Cross-species contamination
+r1_clipped_r2_perfect	157	*	0	0	50M	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,50M,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
diff --git a/testdata/picard/sam/MergeBamAlignment/contam.expected.MOVE_TO_TAG.sam b/testdata/picard/sam/MergeBamAlignment/contam.expected.MOVE_TO_TAG.sam
index 40c06f420..e3a9c761b 100644
--- a/testdata/picard/sam/MergeBamAlignment/contam.expected.MOVE_TO_TAG.sam
+++ b/testdata/picard/sam/MergeBamAlignment/contam.expected.MOVE_TO_TAG.sam
@@ -6,11 +6,11 @@ frag_multiple_primary_2	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATG
 frag_multiple_primary_2	256	chr1	1	15	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:0T0T0C0A0T1C0T0G1	PG:Z:0	RG:Z:0	NM:i:8	UQ:i:240
 frag_secondary_clipped	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:50	PG:Z:0	RG:Z:0	NM:i:0	UQ:i:0
 frag_secondary_clipped	256	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:0T0T0C0A0T1C0T0G1	PG:Z:0	RG:Z:0	NM:i:8	UQ:i:240
-frag_multiple_primary_1	4	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-frag_primary_clipped	4	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-r1_clipped_r2_clipped	109	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-r1_clipped_r2_perfect	109	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-r1_clipped_r2_unmapped	77	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+frag_multiple_primary_1	4	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,0;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+frag_primary_clipped	4	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,0;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_clipped	109	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_perfect	109	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_unmapped	77	*	0	0	*	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PA:Z:chr1,1,20S10M20S,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
 r1_clipped_r2_unmapped	141	*	0	0	*	*	0	0	TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0
-r1_clipped_r2_clipped	157	*	0	0	*	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,20S10M20S,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
-r1_clipped_r2_perfect	157	*	0	0	*	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,50M,30,null;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_clipped	157	*	0	0	*	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,20S10M20S,30,37;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_perfect	157	*	0	0	*	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PA:Z:chr1,51,50M,30,;	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
diff --git a/testdata/picard/sam/MergeBamAlignment/contam.expected.NO_CHANGE.sam b/testdata/picard/sam/MergeBamAlignment/contam.expected.NO_CHANGE.sam
index 5bead4783..13b8d88e5 100644
--- a/testdata/picard/sam/MergeBamAlignment/contam.expected.NO_CHANGE.sam
+++ b/testdata/picard/sam/MergeBamAlignment/contam.expected.NO_CHANGE.sam
@@ -2,15 +2,15 @@
 @SQ	SN:chr1	LN:1000	M5:17522ddd273279f4595f50fea9864734	UR:file:testdata/net/sf/picard/sam/MergeBamAlignment/cliptest.fasta
 @RG	ID:0	SM:Hi,Mom!	PL:ILLUMINA
 @PG	ID:0	VN:1.0	CL:align!	PN:myAligner
-frag_multiple_primary_1	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+frag_multiple_primary_1	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	NM:i:0	CO:Z:Cross-species contamination
 frag_multiple_primary_2	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:50	PG:Z:0	RG:Z:0	NM:i:0	UQ:i:0
 frag_multiple_primary_2	256	chr1	1	15	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:0T0T0C0A0T1C0T0G1	PG:Z:0	RG:Z:0	NM:i:8	UQ:i:240
-frag_primary_clipped	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+frag_primary_clipped	4	chr1	1	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	NM:i:0	CO:Z:Cross-species contamination
 frag_secondary_clipped	0	chr1	1	30	50M	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:50	PG:Z:0	RG:Z:0	NM:i:0	UQ:i:0
 frag_secondary_clipped	256	chr1	1	30	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	MD:Z:0T0T0C0A0T1C0T0G1	PG:Z:0	RG:Z:0	NM:i:8	UQ:i:240
 r1_clipped_r2_clipped	109	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
 r1_clipped_r2_perfect	109	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
 r1_clipped_r2_unmapped	77	*	0	0	20S10M20S	*	0	0	TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
 r1_clipped_r2_unmapped	141	*	0	0	*	*	0	0	TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0
-r1_clipped_r2_clipped	157	*	0	0	20S10M20S	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination
+r1_clipped_r2_clipped	157	*	0	0	20S10M20S	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	NM:i:37	CO:Z:Cross-species contamination
 r1_clipped_r2_perfect	157	*	0	0	50M	*	0	0	TGGAGTGTTAACGTACTCTATTATTGTATTGTTTTTTTTTTGCCCTTAAA	??????????????????????????????????????????????????	PG:Z:0	RG:Z:0	CO:Z:Cross-species contamination