diff --git a/src/main/java/htsjdk/samtools/SamPairUtil.java b/src/main/java/htsjdk/samtools/SamPairUtil.java
index 24d7d62609..94ba6141d7 100644
--- a/src/main/java/htsjdk/samtools/SamPairUtil.java
+++ b/src/main/java/htsjdk/samtools/SamPairUtil.java
@@ -332,6 +332,7 @@ public static void setMateInformationOnSupplementalAlignment( final SAMRecord su
         else {
             supplemental.setAttribute(SAMTag.MC, null);
         }
+        supplemental.setAttribute(SAMTag.MQ, matePrimary.getMappingQuality());
     }
 
     /**