diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 286e009..735563f 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -71,9 +71,11 @@ public class Simulator implements GraphModificationFunctions {
         }
         if (realSequenceCollisionRate > 0.0) {
             if(verbose){System.out.println("Removing wells with anomalous read counts from sequence records");}
-            filterWellsByReadCount(alphaSequences);
-            filterWellsByReadCount(betaSequences);
+            int alphaWellsRemoved = filterWellsByReadCount(alphaSequences);
+            int betaWellsRemoved = filterWellsByReadCount(betaSequences);
             if(verbose){System.out.println("Wells with anomalous read counts removed from sequence records");}
+            if(verbose){System.out.println("Total alpha sequence wells removed: " + alphaWellsRemoved);}
+            if(verbose){System.out.println("Total beta sequence wells removed: " + betaWellsRemoved);}
         }
 
         //construct the graph. For simplicity, going to make
@@ -653,7 +655,7 @@ public class Simulator implements GraphModificationFunctions {
 //    }
 
     //Remove sequences based on occupancy
-    public static void filterByOccupancyThresholds(Map<String, SequenceRecord> wellMap, int low, int high){
+    private static void filterByOccupancyThresholds(Map<String, SequenceRecord> wellMap, int low, int high){
         List<String> noise = new ArrayList<>();
         for(String k: wellMap.keySet()){
             if((wellMap.get(k).getOccupancy() > high) || (wellMap.get(k).getOccupancy() < low)){
@@ -665,7 +667,7 @@ public class Simulator implements GraphModificationFunctions {
         }
     }
 
-    public static void filterByOccupancyAndReadCount(Map<String, SequenceRecord> sequences, int readDepth) {
+    private static void filterByOccupancyAndReadCount(Map<String, SequenceRecord> sequences, int readDepth) {
         List<String> noise = new ArrayList<>();
         for(String k : sequences.keySet()){
             //occupancy times read depth should be more than half the sequence read count if the read error rate is low
@@ -679,7 +681,8 @@ public class Simulator implements GraphModificationFunctions {
         }
     }
 
-    public static void filterWellsByReadCount(Map<String, SequenceRecord> sequences) {
+    private static int filterWellsByReadCount(Map<String, SequenceRecord> sequences) {
+        int count = 0;
         for (String k: sequences.keySet()) {
             //If a sequence has read count R and appears in W wells, then on average its read count in each
             //well should be R/W. Delete any wells where the read count is less than R/2W.
@@ -688,12 +691,14 @@ public class Simulator implements GraphModificationFunctions {
             for (Integer well: sequences.get(k).getWells()) {
                 if (sequences.get(k).getReadCount(well) < threshold) {
                     noise.add(well);
+                    count++;
                 }
             }
             for (Integer well: noise) {
                 sequences.get(k).deleteWell(well);
             }
         }
+        return count;
     }
 
     private static Map<String, String> makeSequenceToSequenceMap(List<String[]> cells, int keySequenceIndex,