diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
index 29fc939fe..b52258895 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
@@ -119,7 +119,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
         intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
         intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000));
-        intervals.add(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
         intervals.add(genomeLocParser.createGenomeLoc("2", 1, 100));
         intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
         intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
@@ -132,7 +131,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008));
         reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
         reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
-        reads.add(buildSAMRecord("end_of_chr1", "1", 249250600, 249250700));
         reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
 
         createBAM(reads);
@@ -244,7 +242,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
         // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
         // outside_intervals: none
-        // end_of_chr1: Primary in 1:249250600-249250621
         // simple20: Primary in 20:10000-10100
 
         Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@@ -259,9 +256,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
         verifyReadMapping(region, "boundary_equal");
 
-        region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
-        verifyReadMapping(region, "end_of_chr1");
-
         region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
         verifyReadMapping(region, "simple20");
     }
@@ -283,7 +277,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
         // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
         // outside_intervals: none
-        // end_of_chr1: Primary in 1:249250600-249250621
         // simple20: Primary in 20:10000-10100
 
         Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@@ -298,9 +291,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
         verifyReadMapping(region, "boundary_equal", "boundary_unequal");
 
-        region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
-        verifyReadMapping(region, "end_of_chr1");
-
         region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
         verifyReadMapping(region, "simple20");
     }
@@ -323,7 +313,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
         // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
         // outside_intervals: none
-        // end_of_chr1: Primary in 1:249250600-249250621
         // simple20: Primary in 20:10000-10100
 
         Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@@ -338,9 +327,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
         region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
         verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np");
 
-        region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
-        verifyReadMapping(region, "end_of_chr1");
-
         region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
         verifyReadMapping(region, "simple20");
     }