diff --git a/pcgr/cna.py b/pcgr/cna.py
index 55a2a18b..e7685aad 100644
--- a/pcgr/cna.py
+++ b/pcgr/cna.py
@@ -142,6 +142,7 @@ def annotate_cna_segments(output_fname: str,
     
     ## Mark copy number amplifications (threshold defined by user) in input
     cna_query_segment_df['aberration_key'] = 'nan'
+    cna_query_segment_df['loss_cond'] = True
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] < n_copy_amplifications,"amp_cond"] = False
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] >= n_copy_amplifications,"amp_cond"] = True
     
@@ -149,6 +150,7 @@ def annotate_cna_segments(output_fname: str,
         cna_query_segment_df.loc[cna_query_segment_df.amp_cond, 'entrezgene'].astype(str) + '_amplification'
     
     ## Mark homozygous deletions in input
+    cna_query_segment_df['amp_cond'] = True
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] > 0,"loss_cond"] = False
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] == 0,"loss_cond"] = True
     
@@ -181,7 +183,7 @@ def annotate_cna_segments(output_fname: str,
             cna_query_segment_df['N_MAJOR'].astype(str), sep=":").str.cat(
                 cna_query_segment_df['N_MINOR'].astype(str), sep=":")
     
-    cna_query_segment_bed['SAMPLE_ID'] = sample_id
+    cna_query_segment_df['SAMPLE_ID'] = sample_id
     cna_query_segment_df.to_csv(output_fname, sep="\t", header=True, index=False)
                 
     return 0