diff --git a/workflow/tests/test_map_reads.py b/workflow/tests/test_map_reads.py
index 5c2ff2be2e5ec0e3675ea3713790743fc3aff344..1cb00d35fa03044218487424796cbd839f1cb64c 100644
--- a/workflow/tests/test_map_reads.py
+++ b/workflow/tests/test_map_reads.py
@@ -18,5 +18,9 @@ def test_map_reads_singleend():
 
 @pytest.mark.integration
 def test_map_reads_pairedend():
-    # Do the same thing for paired end data
-    pass
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam'))
+    aligned_reads_report = test_output_path + 'NCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam.flagstat.qc'
+    samtools_report = open(aligned_reads_report).readlines()
+    assert '72660890 + 0 in total' in samtools_report[0]
+    assert '72053925 + 0 mapped (99.16% : N/A)' in samtools_report[4]
+    assert '71501126 + 0 properly paired (98.40% : N/A)' in samtools_report[8]