diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index d1c96415859ff226cf61c137e5de01abb98dc9a2..b8366f1602294737203c82fe59c6debbb3257d01 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1258,7 +1258,8 @@ public class BamView extends JPanel
         int recordStart = samRecord.getAlignmentStart()+offset;
         int recordEnd   = samRecord.getAlignmentEnd()+offset;
       
-        if(lstStart != recordStart || lstEnd != recordEnd)
+        if(colourByCoverageColour.isSelected() ||
+            lstStart != recordStart || lstEnd != recordEnd)
         { 
           if(colourByCoverageColour.isSelected())
             g2.setColor(getColourByCoverageColour(samRecord));