diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index f91d49aa44ac69c331d3411af2624dc5491298c5..05e6ee953a644cf45b5c309bcc9866aa2f97083f 100644
--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -127,9 +127,9 @@ object BammetricsReport extends ReportBuilder {
         summary, Some(sample), lib).value.getOrElse(0).toString.toLong
       val sb = new StringBuffer()
       if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
-      sb.append((mapped - duplicates) + "\t")
+      sb.append((mapped - duplicates - secondary) + "\t")
       sb.append(duplicates + "\t")
-      sb.append((total - mapped - secondary) + "\t")
+      sb.append((total - mapped) + "\t")
       sb.append(secondary)
       sb.toString
     }