diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index ba2d7e5af6f5d7f6ce483bb170dbb8d2eb95ee46..4b312caba68cb4e01f846fed7d75065bf3008974 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -211,6 +211,10 @@ public class BamView extends JPanel
     this.bamList = bamList;
     this.nbasesInView = nbasesInView;
     
+    // filter out unmapped reads by default
+    setSamRecordFlagPredicate(
+        new SAMRecordFlagPredicate(SAMRecordFlagPredicate.READ_UNMAPPED_FLAG));
+    
     if(reference != null)
     {
       EntryGroup entryGroup = new SimpleEntryGroup();