diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index 5d53f2ef8ab2be24fff67af1fee6504181dac0e7..89dcb6ee678b1b2564b640483a1ec4376582081e 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
@@ -211,7 +211,8 @@ object BiopetFlagstat extends ToolCommand {
     def summary: String = {
       val map = (for (t <- 0 until names.size) yield {
         names(t) -> totalCounts(t)
-      }).toMap
+      }).toMap ++ Map("Singletons" -> crossCounts(names.find(_._2 == "Mapped").map(_._1).getOrElse(-1))(names.find(_._2 == "MateUnmapped").map(_._1).getOrElse(-1))
+      )
 
       ConfigUtils.mapToJson(map).spaces4
     }
diff --git a/biopet-tools/src/test/resources/flagstat_summary.txt b/biopet-tools/src/test/resources/flagstat_summary.txt
index e7984915cab425c8bd94dd0a22eae60e0407f518..da9e68b0a76a10864ad036099966e2dd4c97fe78 100644
--- a/biopet-tools/src/test/resources/flagstat_summary.txt
+++ b/biopet-tools/src/test/resources/flagstat_summary.txt
@@ -11,6 +11,7 @@
     "MateNegativeStrand" : 1,
     "FirstOfPair" : 1,
     "ReadPaired" : 1,
+    "Singletons" : 0,
     "SecondaryOrSupplementary" : 0,
     "SecondOfPair" : 0
 }
\ No newline at end of file