diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 0d1c34ced..c8dbb090d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -30,7 +30,6 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.apache.log4j.Logger;
-import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
@@ -52,18 +51,14 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
+import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
 
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
 import java.util.*;
 
 /**
@@ -175,6 +170,13 @@ public class GenomeAnalysisEngine {
      */
     private Collection<RMDTriplet> referenceMetaDataFiles;
 
+    /**
+     * The threading efficiency monitor we use in the GATK to monitor our efficiency.
+     *
+     * May be null if one isn't active, or hasn't be initialized yet
+     */
+    private ThreadEfficiencyMonitor threadEfficiencyMonitor = null;
+
     /**
      * Set the reference metadata files to use for this traversal.
      * @param referenceMetaDataFiles Collection of files and descriptors over which to traverse.
@@ -252,6 +254,7 @@ public class GenomeAnalysisEngine {
 
         // our microscheduler, which is in charge of running everything
         MicroScheduler microScheduler = createMicroscheduler();
+        threadEfficiencyMonitor = microScheduler.getThreadEfficiencyMonitor();
 
         // create temp directories as necessary
         initializeTempDirectory();
@@ -1003,6 +1006,15 @@ public class GenomeAnalysisEngine {
         return readsDataSource == null ? null : readsDataSource.getCumulativeReadMetrics();
     }
 
+    /**
+     * Return the global ThreadEfficiencyMonitor, if there is one
+     *
+     * @return the monitor, or null if none is active
+     */
+    public ThreadEfficiencyMonitor getThreadEfficiencyMonitor() {
+        return threadEfficiencyMonitor;
+    }
+
     // -------------------------------------------------------------------------------------
     //
     // code for working with Samples database
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index b755cdd77..4becc5a78 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -158,6 +158,14 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
         }
     }
 
+    /**
+     * Return the ThreadEfficiencyMonitor we are using to track our resource utilization, if there is one
+     *
+     * @return the monitor, or null if none is active
+     */
+    public ThreadEfficiencyMonitor getThreadEfficiencyMonitor() {
+        return threadEfficiencyMonitor;
+    }
 
     /**
      * Inform this Microscheduler to use the efficiency monitor used to create threads in subclasses
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index 035252c14..6f3f175a2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
 import org.jets3t.service.S3Service;
 import org.jets3t.service.S3ServiceException;
 import org.jets3t.service.impl.rest.httpclient.RestS3Service;
@@ -141,6 +142,21 @@ public class GATKRunReport {
     @Element(required = true, name = "tag")
     private String tag;
 
+    // -----------------------------------------------------------------
+    // elements related to multi-threading and efficiency
+    // -----------------------------------------------------------------
+
+    @Element(required = true, name = "numThreads")
+    private int numThreads;
+    @Element(required = true, name = "percent_time_running")
+    private String percentTimeRunning;
+    @Element(required = true, name = "percent_time_waiting")
+    private String percentTimeWaiting;
+    @Element(required = true, name = "percent_time_blocking")
+    private String percentTimeBlocking;
+    @Element(required = true, name = "percent_time_waiting_for_io")
+    private String percentTimeWaitingForIO;
+
     public enum PhoneHomeOption {
         /** Disable phone home */
         NO_ET,
@@ -201,12 +217,30 @@ public class GATKRunReport {
 
         // if there was an exception, capture it
         this.mException = e == null ? null : new ExceptionToXML(e);
+
+        numThreads = engine.getArguments().numberOfThreads;
+        percentTimeRunning = getThreadEfficiencyPercent(engine, ThreadEfficiencyMonitor.State.USER_CPU);
+        percentTimeBlocking = getThreadEfficiencyPercent(engine, ThreadEfficiencyMonitor.State.BLOCKING);
+        percentTimeWaiting = getThreadEfficiencyPercent(engine, ThreadEfficiencyMonitor.State.WAITING);
+        percentTimeWaitingForIO = getThreadEfficiencyPercent(engine, ThreadEfficiencyMonitor.State.WAITING_FOR_IO);
     }
 
     public String getID() {
         return id;
     }
 
+    /**
+     * Return a string representing the percent of time the GATK spent in state, if possible.  Otherwise return NA
+     *
+     * @param engine the GATK engine whose threading efficiency info we will use
+     * @param state the state whose occupancy we wish to know
+     * @return a string representation of the percent occupancy of state, or NA is not possible
+     */
+    private String getThreadEfficiencyPercent(final GenomeAnalysisEngine engine, final ThreadEfficiencyMonitor.State state) {
+        final ThreadEfficiencyMonitor tem = engine.getThreadEfficiencyMonitor();
+        return tem == null ? "NA" : String.format("%.2f", tem.getStatePercent(state));
+    }
+
 
     public void postReport(PhoneHomeOption type) {
         logger.debug("Posting report of type " + type);