diff --git a/workflow/scripts/negative_control_check.py b/workflow/scripts/negative_control_check.py
index 069c245..5dde4be 100644
--- a/workflow/scripts/negative_control_check.py
+++ b/workflow/scripts/negative_control_check.py
@@ -43,7 +43,7 @@ def print_tsv(self):
         for row in reader:
             position = int(row["start"]) + int(row["position"])
             depth = int(row["depth"])
-            amplicon_id = int(re.sub("[^0-9]", '', row["amplicon_id"].lstrip(args.primer_prefix)))
+            amplicon_id = int(re.sub("[^0-9]", '', row["amplicon_id"].replace(args.primer_prefix, '')))
 
             #
             genome_coverage.update(position, depth)