diff --git a/clair/call_var.py b/clair/call_var.py
index 8b8a7a7..6ad9794 100644
--- a/clair/call_var.py
+++ b/clair/call_var.py
@@ -20,7 +20,7 @@
 )
 from clair.task.genotype import Genotype, genotype_string_from, genotype_enum_from, genotype_enum_for_task
 from clair.task.variant_length import VariantLength
-from shared.utils import IUPAC_base_to_num_dict as BASE2NUM, IUPAC_base_to_ACGT_base_dict as BASE2ACGT
+from shared.utils import IUPAC_base_to_num_dict as BASE2NUM, IUPAC_base_to_ACGT_base_dict as BASE2ACGT, BASIC_BASES
 import shared.param as param
 
 
@@ -943,6 +943,9 @@ def batch_output(mini_batch, batch_Y, output_config, output_utilities):
         chromosome, position, reference_sequence = chr_pos_seq
         position = int(position)
 
+        if reference_sequence[tensor_position_center] not in BASIC_BASES:
+            continue
+
         # read depth
         read_depth = sum(
             x[tensor_position_center, :, Channel.delete] + x[tensor_position_center, :, Channel.reference]
diff --git a/shared/utils.py b/shared/utils.py
index 61dacaf..d68256e 100644
--- a/shared/utils.py
+++ b/shared/utils.py
@@ -26,6 +26,7 @@
     (0, 1, 2, 3, 3, 0, 1, 1, 0, 2, 0, 1, 0, 0, 0)
 ))
 
+BASIC_BASES = set("ACGTU")
 
 def is_file_exists(file_name, suffix=""):
     if not isinstance(file_name, str) or not isinstance(suffix, str):