diff --git a/neat/models/mutation_model.py b/neat/models/mutation_model.py
index 9c7a3074..ffc6ddcf 100644
--- a/neat/models/mutation_model.py
+++ b/neat/models/mutation_model.py
@@ -75,8 +75,6 @@ def __init__(self,
         self.variant_probs = variant_probs
         self.transition_matrix = transition_matrix
         self.is_cancer = is_cancer
-        self.all_dels = []
-        self.all_ins = []
 
     def get_mutation_type(self, rng: Generator) -> VariantTypes:
         """
@@ -125,7 +123,6 @@ def generate_snv(self, trinucleotide: Seq, reference_location: int, rng: Generat
         # Now pick a random alternate, weighted by the probabilities
         alt = rng.choice(ALLOWED_NUCL, p=transition_probs)
         temp_snv = SingleNucleotideVariant(reference_location, alt=alt)
-        self.all_ins.append(temp_snv)
         return temp_snv
 
     def generate_insertion(self, location: int, ref: Seq, rng: Generator) -> Insertion:
@@ -158,5 +155,4 @@ def generate_deletion(self, location: int, rng: Generator) -> Deletion:
         # Plus one so we make sure to grab the first base too.
         # Note: if we happen to go past the end of the sequence, it will just be shorter.
         temp_del = Deletion(location, length)
-        self.all_dels.append(temp_del)
         return temp_del
diff --git a/neat/read_simulator/utils/generate_variants.py b/neat/read_simulator/utils/generate_variants.py
index 4a29962b..6f3a5af6 100644
--- a/neat/read_simulator/utils/generate_variants.py
+++ b/neat/read_simulator/utils/generate_variants.py
@@ -238,6 +238,8 @@ def generate_variants(
                 location = local_location + ref_start  # relative to overall contig
                 if local_location == 0:
                     continue
+                # local_location is the center (mutated) base returned by sample_trinucs;
+                # shift slice left by 1 so trinuc[0]=5' flank, trinuc[1]=ref base, trinuc[2]=3' flank
                 trinuc = reference[local_location-1: local_location+2].seq.upper()
                 disallowed_chars = False
                 for letter in trinuc: