diff --git a/python/obitools3/commands/uniq.pyx b/python/obitools3/commands/uniq.pyx
index 851a5bd..28c7a61 100644
--- a/python/obitools3/commands/uniq.pyx
+++ b/python/obitools3/commands/uniq.pyx
@@ -243,7 +243,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     # Keep columns that are going to be used a lot in variables 
     i_seq_col = view[NUC_SEQUENCE_COLUMN]
     i_id_col = view[ID_COLUMN]
-    i_taxid_col = view[b"taxid"]
+    if b"taxid" in view:
+        i_taxid_col = view[b"taxid"]
     if b"taxid_dist" in view:
         i_taxid_dist_col = view[b"taxid_dist"]
 
@@ -380,8 +381,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
         if mergeIds:
             o_merged_col[o_idx] = [view[idx].id for idx in merged_sequences]
 
-        if COUNT_COLUMN not in o_seq or o_seq[COUNT_COLUMN] is None:
-            o_seq[COUNT_COLUMN] = 1
+        o_seq[COUNT_COLUMN] = 0
 
         if b"taxid_dist" in u_seq and i_taxid_dist_col[u_idx] is not None:
             taxid_dist_dict = i_taxid_dist_col[u_idx]
@@ -460,7 +460,11 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
                     o_seq[key] = None
 
         o_idx += 1
-     
+    
+    # Deletes quality column if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not)
+    if QUALITY_COLUMN in view:
+        o_view.delete_column(QUALITY_COLUMN)
+    
     if taxonomy is not None:
         logger("info", "Merging taxonomy classification")
         merge_taxonomy_classification(o_view, taxonomy)