diff --git a/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java b/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
index 509ec887b..c8b1d443c 100755
--- a/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
+++ b/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
@@ -79,7 +79,7 @@ public class FastqToBam extends CommandLineProgram {
                 sr2.setReadPairedFlag(true);
                 sr2.setAttribute("RG", READ_GROUP_NAME);
                 sr2.setFirstOfPairFlag(false);
-                sr2.setSecondOfPairFlag(false);
+                sr2.setSecondOfPairFlag(true);
                 sr2.setMateUnmappedFlag(true);
             }