diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 69bc80a771aff10fa8bd9070fd9d31269ffd9aa8..1dea2a441287953ff480bb3fd10c5fff87794995 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -956,7 +956,11 @@ sub remove_mapping_data{
 
   $sql = "DELETE from mapping";
   $sth = $self->xref->dbc->prepare($sql);
-  $sth->execute(); 
+  $sth->execute();
+
+  $sql = "DELETE from alt_allele";
+  $sth = $self->xref->dbc->prepare($sql);
+  $sth->execute();
   return;
 }