diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java
new file mode 100755
index 000000000..1e12e9af6
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java
@@ -0,0 +1,88 @@
+package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
+
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.playground.utils.report.GATKReport.GATKReport;
+import org.broadinstitute.sting.utils.BaseUtils;
+
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Computes the read error rate per position in read (in the original 5'->3' orientation that the read had coming off the machine)
+ */
+public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
+    @Output PrintStream out;
+    @Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling (default: 0)", required=false) public Integer MIN_BASE_QUAL = 0;
+    @Argument(fullName="min_mapping_quality_score", shortName="mmq", doc="Minimum read mapping quality required to consider a read for calling (default: 0)", required=false) public Integer MIN_MAPPING_QUAL = 0;
+
+    private GATKReport report;
+    private String reportName = "ErrorRatePerCycle";
+    private String reportDescription = "The error rate per sequenced position in the reads";
+
+    public void initialize() {
+        report = new GATKReport();
+
+        report.addTable(reportName, reportDescription);
+        report.getTable(reportName).addPrimaryKey("cycle");
+
+        for (SAMReadGroupRecord rg : this.getToolkit().getSAMFileHeader().getReadGroups()) {
+            String readGroupId = rg.getReadGroupId();
+
+            report.getTable(reportName).addColumn("mismatches." + readGroupId, 0, false);
+            report.getTable(reportName).addColumn(   "qualsum." + readGroupId, 0, false);
+            report.getTable(reportName).addColumn(    "counts." + readGroupId, 0, false);
+            report.getTable(reportName).addColumn( "errorrate." + readGroupId, 0.0f);
+            report.getTable(reportName).addColumn(   "qualavg." + readGroupId, 0.0f);
+        }
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        List<Integer> offsets = context.getOffsets();
+        List<SAMRecord> reads = context.getReads();
+
+        for (int i = 0; i < offsets.size(); i++) {
+            int offset = offsets.get(i);
+
+            if (reads.get(i).getMappingQuality() >= MIN_MAPPING_QUAL && reads.get(i).getBaseQualities()[offset] >= MIN_BASE_QUAL) {
+                char readBase = reads.get(i).getReadString().charAt(offset);
+
+                int refIndex = ref.getBaseIndex();
+                int readIndex = BaseUtils.simpleBaseToBaseIndex(readBase);
+
+                if (!reads.get(i).getReadNegativeStrandFlag() && (!reads.get(i).getReadPairedFlag() || reads.get(i).getFirstOfPairFlag())) {
+                    String readGroupId = reads.get(i).getReadGroup().getReadGroupId();
+
+                    if (refIndex != readIndex) {
+                        report.getTable(reportName).increment(offset, "mismatches." + readGroupId);
+                    }
+                    report.getTable(reportName).add(offset, "qualsum." + readGroupId, (int) reads.get(i).getBaseQualities()[offset]);
+                    report.getTable(reportName).increment(offset, "counts." + readGroupId);
+                }
+            }
+        }
+
+        return null;
+    }
+
+    public Integer reduceInit() { return null; }
+
+    public Integer reduce(Integer value, Integer sum) { return null; }
+
+    public void onTraversalDone(Integer sum) {
+        for (SAMReadGroupRecord rg : this.getToolkit().getSAMFileHeader().getReadGroups()) {
+            String readGroupId = rg.getReadGroupId();
+            
+            report.getTable(reportName).divideColumns("errorrate." + readGroupId, "mismatches." + readGroupId, "counts." + readGroupId);
+            report.getTable(reportName).divideColumns(  "qualavg." + readGroupId,    "qualsum." + readGroupId, "counts." + readGroupId);
+        }
+
+        report.print(out);
+    }
+}