diff --git a/src/main/java/Plate.java b/src/main/java/Plate.java
index 3ba7a1b..b81a140 100644
--- a/src/main/java/Plate.java
+++ b/src/main/java/Plate.java
@@ -162,15 +162,18 @@ public class Plate {
     public Map<String, SequenceRecord> countSequences(Integer readDepth, Double readErrorRate,
                                                        Double errorCollisionRate, Double realSequenceCollisionRate, int... sIndices) {
         SequenceType[] sequenceTypes = EnumSet.allOf(SequenceType.class).toArray(new SequenceType[0]);
-        //Map of all sequences read. Keys are sequences, values are ways sequence has been misread.
+        //Map of all real sequences read. Keys are sequences, values are ways sequence has been misread.
         Map<String, List<String>> sequencesAndMisreads = new HashMap<>();
+        //Map of all sequences read. Keys are sequences, values are associated SequenceRecords
         Map<String, SequenceRecord> sequenceMap = new LinkedHashMap<>();
         for (int well = 0; well < size; well++) {
-            for (String[] cell : wells.get(well)) {
-                for (int sIndex : sIndices) {
+            for (String[] cell: wells.get(well)) {
+                for (int sIndex: sIndices) {
+                    //the sequence being read
                     String currentSequence = cell[sIndex];
                     //skip dropout sequences, which have value -1
                     if (!"-1".equals(currentSequence)) {
+                        //keep rereading the sequence until the read depth is reached
                         for (int j = 0; j < readDepth; j++) {
                             //The sequence is misread
                             if (rand.nextDouble() < readErrorRate) {
@@ -180,7 +183,7 @@ public class Plate {
                                 }
                                 //The specific misread hasn't happened before
                                 if (rand.nextDouble() >= errorCollisionRate || sequencesAndMisreads.get(currentSequence).size() == 0) {
-                                    //The misread doesn't collide with a real sequence already on the plate
+                                    //The misread doesn't collide with a real sequence already on the plate and some sequences have already been read
                                     if(rand.nextDouble() >= realSequenceCollisionRate || !sequenceMap.isEmpty()){
                                         StringBuilder spurious = new StringBuilder(currentSequence);
                                         for (int k = 0; k <= sequencesAndMisreads.get(currentSequence).size(); k++) {
@@ -202,9 +205,11 @@ public class Plate {
                                             wrongSequence = sequencesAndMisreads.keySet().toArray(new String[0])[index];
                                             //make sure it's not accidentally the *right* sequence
                                             //Also that it's not a wrong sequence already in the misread list
-                                        } while(cell[sIndex].equals(wrongSequence) || sequencesAndMisreads.get(currentSequence).contains(wrongSequence));
+                                        } while(currentSequence.equals(wrongSequence) || sequencesAndMisreads.get(currentSequence).contains(wrongSequence));
+                                        //update the SequenceRecord for wrongSequence
                                         sequenceMap.get(wrongSequence).addRead(well);
-
+                                        //add wrongSequence to the misreads for currentSequence
+                                        sequencesAndMisreads.get(currentSequence).add(wrongSequence);
                                     }
                                 }
                             }