diff --git a/itests/case-base_single_cell.sh b/itests/case-base_single_cell.sh
index 01535a456..221a7f041 100755
--- a/itests/case-base_single_cell.sh
+++ b/itests/case-base_single_cell.sh
@@ -36,8 +36,8 @@ assert "cat base_single_cell.vdjcontigs.assembleContigs.report.json | head -n 1
 
 assert "mixcr exportClones --no-header base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "7"
 assert "mixcr exportClones --no-header --split-by-tags Cell base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "7"
-assert "mixcr exportClones --no-header --split-by-tags Molecule base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "82"
-assert "mixcr exportClones --no-header -tags Molecule base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "82"
+assert "mixcr exportClones --no-header --split-by-tags Molecule base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "92"
+assert "mixcr exportClones --no-header -tags Molecule base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "92"
 assert "mixcr exportClones --no-header --drop-default-fields -cellGroup base_single_cell.vdjcontigs.assembledCells.clns | sort | uniq | wc -l" "3"
 
 # I didn't found normal way to round up a number in bash
diff --git a/itests/case008.sh b/itests/case008.sh
index 80eafe2a8..dd114dbc6 100755
--- a/itests/case008.sh
+++ b/itests/case008.sh
@@ -30,9 +30,9 @@ mixcr analyze --verbose generic-amplicon \
   CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case8
 
 assert "cat case8.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241313"
-assert "cat case8.assemble.report.json | head -n 1 | jq -r .readsInClones" "200730"
+assert "cat case8.assemble.report.json | head -n 1 | jq -r .readsInClones" "200731"
 assert "cat case8.assemble.report.json | head -n 1 | jq -r .clones" "25653"
 assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .longestContigLength" "499"
-assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3544"
+assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3543"
 assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .assemblePrematureTerminationEvents" "4"
 assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25653"
diff --git a/itests/case009.sh b/itests/case009.sh
index 9366ae8c2..26b06cc67 100755
--- a/itests/case009.sh
+++ b/itests/case009.sh
@@ -31,8 +31,8 @@ mixcr analyze --verbose generic-amplicon \
   CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case9
 
 assert "cat case9.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241313"
-assert "cat case9.assemble.report.json | head -n 1 | jq -r .readsInClones" "200730"
+assert "cat case9.assemble.report.json | head -n 1 | jq -r .readsInClones" "200731"
 assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .longestContigLength" "499"
-assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3544"
+assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3543"
 assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .assemblePrematureTerminationEvents" "4"
 assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25653"