diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
index 30da069a41..3f6e2bc2cb 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
@@ -698,15 +698,10 @@ case class ReferenceRegion(
         start,
         other.start,
         newRegionStrand))
-    } else if (end > other.end) {
-      Iterable(ReferenceRegion(referenceName,
-        start,
-        other.end,
-        newRegionStrand))
     } else {
       Iterable.empty[ReferenceRegion]
     }
-    val second = if (other.start > start && end > other.end) {
+    val second = if (end > other.end) {
       Iterable(ReferenceRegion(referenceName,
         other.end,
         end,
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
index 11cdf9a3aa..b082cfeda0 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
@@ -264,13 +264,13 @@ class ReferenceRegionSuite extends FunSuite {
     // right end unstranded
     assert(ReferenceRegion("chr0", 10, 100, Strand.FORWARD).subtract(ReferenceRegion("chr0", 90, 150, Strand.REVERSE), false) === List(ReferenceRegion("chr0", 10, 90)))
     // left end unstranded
-    assert(ReferenceRegion("chr0", 90, 150, Strand.REVERSE).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), false) === List(ReferenceRegion("chr0", 90, 100)))
+    assert(ReferenceRegion("chr0", 90, 150, Strand.REVERSE).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), false) === List(ReferenceRegion("chr0", 100, 150)))
     // contained unstranded
     assert(ReferenceRegion("chr0", 2, 150, Strand.REVERSE).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), false) === List(ReferenceRegion("chr0", 2, 10), ReferenceRegion("chr0", 100, 150)))
     // right end stranded
     assert(ReferenceRegion("chr0", 10, 100, Strand.FORWARD).subtract(ReferenceRegion("chr0", 90, 150, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 10, 90, Strand.FORWARD)))
     // left end stranded
-    assert(ReferenceRegion("chr0", 90, 150, Strand.FORWARD).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 90, 100, Strand.FORWARD)))
+    assert(ReferenceRegion("chr0", 90, 150, Strand.FORWARD).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 100, 150, Strand.FORWARD)))
     // contained stranded
     assert(ReferenceRegion("chr0", 2, 150, Strand.FORWARD).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 2, 10, Strand.FORWARD), ReferenceRegion("chr0", 100, 150, Strand.FORWARD)))