diff --git a/barcodeforge/generate_barcodes.py b/barcodeforge/generate_barcodes.py
index f267478..65e20f3 100755
--- a/barcodeforge/generate_barcodes.py
+++ b/barcodeforge/generate_barcodes.py
@@ -196,7 +196,7 @@ def check_mutation_chain(df_barcodes: pd.DataFrame) -> pd.DataFrame:
             else:
                 # combining leads to already existing mutation
                 # just add in that mutation
-                df_barcodes.loc[lin_seq.index, sm[2]] = 1
+                df_barcodes.loc[lin_seq.index, sm[2]] += 1
             # remove constituent mutations
             df_barcodes.loc[lin_seq.index, sm[0:2]] -= 1
         # drop all unused mutations
@@ -207,6 +207,8 @@ def check_mutation_chain(df_barcodes: pd.DataFrame) -> pd.DataFrame:
         # in case mutation path leads to a return to the reference.
         df_barcodes = reversion_checking(df_barcodes)
         seq_muts = identify_chains(df_barcodes)
+    # The barcode should be a binary sparse matrix
+    assert df_barcodes.isin([0, 1]).all(axis=None), "Barcode matrix should be binary"
     return df_barcodes
 
 
diff --git a/tests/test_generate_barcodes.py b/tests/test_generate_barcodes.py
index 0483c58..b078650 100644
--- a/tests/test_generate_barcodes.py
+++ b/tests/test_generate_barcodes.py
@@ -91,6 +91,35 @@ def test_check_mutation_chain(sample_barcode_data):
     assert isinstance(chained_df, pd.DataFrame)
 
 
+def test_check_mutation_chain_repetitve_mutations():
+    sample_barcode_data = pd.DataFrame(
+        {"A225G": [1], "A225T": [1], "C225A": [1], "G225T": [1], "T225C": [2]},
+        index=["lineage"],
+    )
+    chained_df = check_mutation_chain(sample_barcode_data.copy())
+    df_barcodes_ideal = pd.DataFrame(
+        {"A225C": [1]},
+        index=["lineage"],
+    )
+    pd.testing.assert_frame_equal(chained_df, df_barcodes_ideal)
+
+
+def test_check_mutation_chain_non_binary_values():
+    sample_barcode_data = pd.DataFrame(
+        {
+            "A225G": [1],
+            "A225T": [1],
+            "C225A": [1],
+            "G225T": [1],
+            "T225C": [2],
+            "C123A": [2],
+        },
+        index=["lineage"],
+    )
+    with pytest.raises(AssertionError, match="Barcode matrix should be binary"):
+        check_mutation_chain(sample_barcode_data.copy())
+
+
 def test_replace_underscore_with_dash():
     data = {"value": [1, 2]}
     df = pd.DataFrame(data, index=["lineage_A", "lineage_B"])