diff --git a/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java b/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
index c1cb47b72..c66762b42 100644
--- a/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
+++ b/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
@@ -240,7 +240,7 @@ private void collectReadData(final SAMRecord record) {
                         }
                     } else if(doRefMetrics) {
                         metrics.PF_READS_ALIGNED++;
-                        if (!record.getProperPairFlag()) metrics.PF_READS_IMPROPER_PAIRS++;
+                        if (record.getReadPairedFlag() && !record.getProperPairFlag()) metrics.PF_READS_IMPROPER_PAIRS++;
                         if (!record.getReadNegativeStrandFlag()) numPositiveStrand++;
                         if (record.getReadPairedFlag() && !record.getMateUnmappedFlag()) {
                             metrics.READS_ALIGNED_IN_PAIRS++;