diff --git a/ld-validation/src/main/java/org/dash/valid/LinkageDisequilibriumAnalyzer.java b/ld-validation/src/main/java/org/dash/valid/LinkageDisequilibriumAnalyzer.java
index ff8694e..03e1f4f 100644
--- a/ld-validation/src/main/java/org/dash/valid/LinkageDisequilibriumAnalyzer.java
+++ b/ld-validation/src/main/java/org/dash/valid/LinkageDisequilibriumAnalyzer.java
@@ -24,9 +24,7 @@
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.LinkedHashMap;
 import java.util.List;
-import java.util.Map;
 import java.util.logging.Handler;
 import java.util.logging.LogManager;
 import java.util.logging.Logger;
@@ -89,7 +87,7 @@ private static void analyzeGLStringFiles(String[] filenames) throws IOException
 	}
 	
 	public static List<Sample> analyzeGLStringFile(String name, BufferedReader reader) throws IOException {
-		LinkedHashMap<String, String> glStrings = GLStringUtilities.readGLStringFile(name, reader);
+		List<LinkageDisequilibriumGenotypeList> glStrings = GLStringUtilities.readGLStringFile(name, reader);
 		
 		List<Sample> samplesList = detectLinkages(glStrings);
 		
@@ -100,7 +98,7 @@ public static List<Sample> analyzeGLStringFile(String name, BufferedReader reade
 	 * @param filename
 	 */
 	public static void analyzeGLStringFile(String filename) throws IOException {				
-		LinkedHashMap<String, String> glStrings = GLStringUtilities.readGLStringFile(filename);
+		List<LinkageDisequilibriumGenotypeList> glStrings = GLStringUtilities.readGLStringFile(filename);
 		List<Sample> samplesList = null;
 		
 		samplesList = detectLinkages(glStrings);
@@ -111,7 +109,6 @@ public static void analyzeGLStringFile(String filename) throws IOException {
 			HaplotypePairWriter.getInstance().reportDetectedLinkages(findings);
 			CommonWellDocumentedWriter.getInstance().reportCommonWellDocumented(findings);
 			DetectedFindingsWriter.getInstance().reportDetectedFindings(findings);
-			//SummaryWriter.getInstance().reportDetectedLinkages(findings);
 		}
 		
 		SamplesList allSamples = new SamplesList();
@@ -125,24 +122,11 @@ public static void analyzeGLStringFile(String filename) throws IOException {
 	 * @throws IOException 
 	 * @throws SecurityException 
 	 */
-	private static List<Sample> detectLinkages(Map<String, String> glStrings) {
-		LinkageDisequilibriumGenotypeList linkedGLString;
-		String glString;
+	private static List<Sample> detectLinkages(List<LinkageDisequilibriumGenotypeList> glStrings) {
 		List<Sample> samplesList = new ArrayList<Sample>();
 		
 		int idx = 1;
-		for (String key : glStrings.keySet()) {
-			glString = glStrings.get(key);
-			String submittedGlString = glString;
-			
-			if (!GLStringUtilities.validateGLStringFormat(glString)) {
-				glString = GLStringUtilities.fullyQualifyGLString(glString);
-			}
-			
-			MultilocusUnphasedGenotype mug = GLStringUtilities.convertToMug(glString);
-			linkedGLString = new LinkageDisequilibriumGenotypeList(key, mug);
-			
-			linkedGLString.setSubmittedGlString(submittedGlString);
+		for (LinkageDisequilibriumGenotypeList linkedGLString : glStrings) {
 			
 			List<Haplotype> knownHaplotypes = GLStringUtilities.buildHaplotypes(linkedGLString);
 			
diff --git a/ld-validation/src/main/java/org/dash/valid/Sample.java b/ld-validation/src/main/java/org/dash/valid/Sample.java
index d152924..8abc1bb 100644
--- a/ld-validation/src/main/java/org/dash/valid/Sample.java
+++ b/ld-validation/src/main/java/org/dash/valid/Sample.java
@@ -20,6 +20,11 @@ public String getId() {
 		return getGenotypeList().getId();
 	}
 	
+	@XmlAttribute(name="note")
+	public String getNote() {
+		return getGenotypeList().getNote();
+	}
+	
 	@XmlElement(name="processed-gl-string")
 	public String getProcessedGlString() {
 		return getGenotypeList().getGLString().equals(getGenotypeList().getSubmittedGlString()) ? null : getGenotypeList().getGLString();
diff --git a/ld-validation/src/main/java/org/dash/valid/gl/GLStringUtilities.java b/ld-validation/src/main/java/org/dash/valid/gl/GLStringUtilities.java
index 3bcbd5a..39d52ae 100644
--- a/ld-validation/src/main/java/org/dash/valid/gl/GLStringUtilities.java
+++ b/ld-validation/src/main/java/org/dash/valid/gl/GLStringUtilities.java
@@ -32,7 +32,6 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Set;
 import java.util.StringTokenizer;
@@ -416,11 +415,11 @@ public static String fillLocus(Locus locus, String segment) {
 		return segment;
 	}
 	
-	public static LinkedHashMap<String, String> readGLStringFile(String name, BufferedReader reader) {
-		LinkedHashMap<String, String> glStrings = null;
+	public static List<LinkageDisequilibriumGenotypeList> readGLStringFile(String name, BufferedReader reader) {
+		List<LinkageDisequilibriumGenotypeList> linkedGLStrings = null;
 		
 		try {
-			glStrings = parseGLStringFile(name, reader);
+			linkedGLStrings = parseGLStringFile(name, reader);
 		} catch (IOException e) {
 			LOGGER.severe("Problem reading GL String file: " + name);
 			e.printStackTrace();
@@ -430,12 +429,12 @@ public static LinkedHashMap<String, String> readGLStringFile(String name, Buffer
 				e.printStackTrace();
 		 }
 		
-		return glStrings;
+		return linkedGLStrings;
 	}
 
-	public static LinkedHashMap<String, String> readGLStringFile(String filename) {
+	public static List<LinkageDisequilibriumGenotypeList> readGLStringFile(String filename) {
 		BufferedReader reader = null;
-		LinkedHashMap<String, String> glStrings = null;
+		List<LinkageDisequilibriumGenotypeList> linkedGLStrings = null;
 
 		try {
 			InputStream stream = GLStringUtilities.class.getClassLoader()
@@ -446,7 +445,7 @@ public static LinkedHashMap<String, String> readGLStringFile(String filename) {
 			
 			reader = new BufferedReader(new InputStreamReader(stream));
 
-			glStrings = parseGLStringFile(filename, reader);
+			linkedGLStrings = parseGLStringFile(filename, reader);
 			
 		} catch (FileNotFoundException e) {
 			LOGGER.severe("Couldn't find GL String file: " + filename);
@@ -465,14 +464,15 @@ public static LinkedHashMap<String, String> readGLStringFile(String filename) {
 				e.printStackTrace();
 			}
 		}
-
-		return glStrings;
+		
+		return linkedGLStrings;
 	}
 
-	private static LinkedHashMap<String, String> parseGLStringFile(String filename,
+	private static List<LinkageDisequilibriumGenotypeList> parseGLStringFile(String filename,
 			BufferedReader reader)
 			throws IOException, ParserConfigurationException, SAXException {
-		LinkedHashMap<String, String> glStrings = new LinkedHashMap<String, String>();
+		List<LinkageDisequilibriumGenotypeList> linkedGLStrings = new ArrayList<LinkageDisequilibriumGenotypeList>();
+
 
 		if (filename.endsWith(GLStringConstants.XML) || filename.endsWith(GLStringConstants.HML)) {
 		    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -492,29 +492,63 @@ private static LinkedHashMap<String, String> parseGLStringFile(String filename,
 		    		if (j > 0) glString.append(GLStringConstants.GENE_DELIMITER);
 		    		glString.append(((Element) alleleAssignment.getElementsByTagName(GLStringConstants.GL_STRING_ELEMENT).item(0)).getTextContent().trim());
 		    	}
-		    	glStrings.put(sampleId,  glString.toString());
+		    	
+		    	linkedGLStrings.add(inflateGenotypeList(sampleId, glString.toString(), null));
 		    }
 		}
 		else {
 			String line;
 			String[] parts = null;
 			int lineNumber = 0;
+			String glString;
+			String id;
+			String note = null;			
+			
 			while ((line = reader.readLine()) != null) {
+				lineNumber++;
+
 				parts = line.split(FILE_DELIMITER_REGEX);
+				
 				if (parts.length == 1) {
-					glStrings.put(filename + "-" + lineNumber, parts[0]);
-				} else if (parts.length == 2) {
-					glStrings.put(parts[0], parts[1]);
-				} else {
+					id = filename + "-" + (lineNumber - 1);
+					glString = parts[0];
+				} else if (parts.length >= 2) {
+					id = parts[0];
+					glString = parts[1];
+					
+					if (parts.length == 3) note = parts[2];
+				}
+				else {
 					LOGGER.warning("Unexpected line format at line "
-							+ lineNumber + ": " + filename);
+							+ (lineNumber - 1) + ": " + filename);
+					
+					continue;
 				}
-	
-				lineNumber++;
+				
+				linkedGLStrings.add(inflateGenotypeList(id, glString, note));
+					
 			}
 		}
+				
+		return linkedGLStrings;
+	}
+	
+	private static LinkageDisequilibriumGenotypeList inflateGenotypeList(String id, String glString, String note) {
+		LinkageDisequilibriumGenotypeList linkedGLString;
+		
+		String submittedGlString = glString;
+		
+		if (!GLStringUtilities.validateGLStringFormat(glString)) {
+			glString = GLStringUtilities.fullyQualifyGLString(glString);
+		}
+		
+		MultilocusUnphasedGenotype mug = GLStringUtilities.convertToMug(glString);
+		linkedGLString = new LinkageDisequilibriumGenotypeList(id, mug);
+		
+		linkedGLString.setSubmittedGlString(submittedGlString);
+		linkedGLString.setNote(note);
 		
-		return glStrings;
+		return linkedGLString;
 	}
 
 	public static MultilocusUnphasedGenotype convertToMug(String glString) {
diff --git a/ld-validation/src/main/java/org/dash/valid/gl/LinkageDisequilibriumGenotypeList.java b/ld-validation/src/main/java/org/dash/valid/gl/LinkageDisequilibriumGenotypeList.java
index 011c0bc..01ce9a9 100644
--- a/ld-validation/src/main/java/org/dash/valid/gl/LinkageDisequilibriumGenotypeList.java
+++ b/ld-validation/src/main/java/org/dash/valid/gl/LinkageDisequilibriumGenotypeList.java
@@ -46,6 +46,7 @@
 public class LinkageDisequilibriumGenotypeList {
 	private String id;
 	private String glString;
+	private String note;
 	private String submittedGlString;
 
 	private MultilocusUnphasedGenotype mug;
@@ -105,6 +106,14 @@ public LinkageDisequilibriumGenotypeList(String id, MultilocusUnphasedGenotype m
 		}
 	}
 	
+	public String getNote() {
+		return note;
+	}
+	
+	public void setNote(String note) {
+		this.note = note;
+	}
+	
 	public String getSubmittedGlString() {
 		return submittedGlString;
 	}
diff --git a/ld-validation/src/main/resources/schema/LinkageFindings.xsd b/ld-validation/src/main/resources/schema/LinkageFindings.xsd
index 46d83ca..cab0b32 100644
--- a/ld-validation/src/main/resources/schema/LinkageFindings.xsd
+++ b/ld-validation/src/main/resources/schema/LinkageFindings.xsd
@@ -15,6 +15,7 @@
 				<xs:element name="processed-gl-string" type="xs:string" minOccurs="0"/>
 			</xs:sequence>
 			<xs:attribute name="id" type="xs:string"/>
+			<xs:attribute name="note" type="xs:string"/>
 		</xs:complexType>
 	</xs:element>
     <xs:element name="gl-freq">
diff --git a/ld-validation/src/test/java/org/dash/LinkageDisequilibriumAnalyzerTest.java b/ld-validation/src/test/java/org/dash/LinkageDisequilibriumAnalyzerTest.java
index d69ebf6..ef6f8a0 100644
--- a/ld-validation/src/test/java/org/dash/LinkageDisequilibriumAnalyzerTest.java
+++ b/ld-validation/src/test/java/org/dash/LinkageDisequilibriumAnalyzerTest.java
@@ -22,7 +22,6 @@
 package org.dash;
 
 import java.io.IOException;
-import java.util.LinkedHashMap;
 import java.util.List;
 
 import org.dash.valid.HLALinkageDisequilibrium;
@@ -49,10 +48,10 @@ public void testLinkageReportingExamples() {
 	
 	@Test
 	public void testLinkageReportingMugs() throws IOException {
-		LinkedHashMap<String, String> glStrings = GLStringUtilities.readGLStringFile("fullyQualifiedExample.txt");
+		List<LinkageDisequilibriumGenotypeList> glStrings = GLStringUtilities.readGLStringFile("fullyQualifiedExample.txt");
 		
-		for (String key : glStrings.keySet()) {
-			MultilocusUnphasedGenotype mug = GLStringUtilities.convertToMug(glStrings.get(key));
+		for (LinkageDisequilibriumGenotypeList linkedGLString : glStrings) {
+			MultilocusUnphasedGenotype mug = GLStringUtilities.convertToMug(linkedGLString.getGLString());
 			
 			assertNotNull(mug);
 			
diff --git a/ld-validation/src/test/java/org/dash/gl/GLStringTest.java b/ld-validation/src/test/java/org/dash/gl/GLStringTest.java
index bc19681..fbd333e 100644
--- a/ld-validation/src/test/java/org/dash/gl/GLStringTest.java
+++ b/ld-validation/src/test/java/org/dash/gl/GLStringTest.java
@@ -25,8 +25,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.util.LinkedHashMap;
-import java.util.Set;
+import java.util.List;
 
 import org.dash.valid.Locus;
 import org.dash.valid.gl.GLStringUtilities;
@@ -47,20 +46,13 @@ public class GLStringTest extends TestCase {
 	
 	@Before
 	public void setUp() throws IOException {
-		LinkedHashMap<String, String> validGLStrings = GLStringUtilities.readGLStringFile("fullyQualifiedExample.txt");
+		List<LinkageDisequilibriumGenotypeList> validGLStrings = GLStringUtilities.readGLStringFile("fullyQualifiedExample.txt");
+				
+		glString = validGLStrings.get(0);
 		
-		Set<String> keys = validGLStrings.keySet();
+		List<LinkageDisequilibriumGenotypeList> strictGLStrings = GLStringUtilities.readGLStringFile("strictExample.txt");
 		
-		for (String key : keys) {
-			glString = new LinkageDisequilibriumGenotypeList(key, GLStringUtilities.fullyQualifyGLString(validGLStrings.get(key)));
-		}
-		
-		LinkedHashMap<String, String> strictGLStrings = GLStringUtilities.readGLStringFile("strictExample.txt");
-		
-		keys = strictGLStrings.keySet();
-		String key = keys.iterator().next();
-		
-		STRICT_GL_STRING = strictGLStrings.get(key);
+		STRICT_GL_STRING = strictGLStrings.get(0).getGLString();
 	}
 	
 	@Test
diff --git a/ld-validation/src/test/java/org/dash/gl/GLStringUtilitiesTest.java b/ld-validation/src/test/java/org/dash/gl/GLStringUtilitiesTest.java
index 92f035e..a3ebd3f 100644
--- a/ld-validation/src/test/java/org/dash/gl/GLStringUtilitiesTest.java
+++ b/ld-validation/src/test/java/org/dash/gl/GLStringUtilitiesTest.java
@@ -22,7 +22,6 @@
 package org.dash.gl;
 
 import java.io.IOException;
-import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Set;
 
@@ -30,6 +29,7 @@
 import org.dash.valid.freq.HLAFrequenciesLoader;
 import org.dash.valid.gl.GLStringConstants;
 import org.dash.valid.gl.GLStringUtilities;
+import org.dash.valid.gl.LinkageDisequilibriumGenotypeList;
 import org.junit.Test;
 import org.nmdp.gl.MultilocusUnphasedGenotype;
 
@@ -56,6 +56,7 @@ public class GLStringUtilitiesTest extends TestCase {
 	private static final String VALID_GL_STRING_MAC = "HLA-A*01:01/HLA-A*01:02+HLA-A*26:01^HLA-C*01:01/HLA-C*01:03+HLA-C*04:01";
 	private static final String TAB_DELIMITED = "TAB_DELIMITED";
 	private static final String COMMA_DELIMITED = "COMMA_DELIMITED";
+	private static final String MY_NOTE = "My Note";
 	
 	@Test
 	public void testParse() {
@@ -79,25 +80,26 @@ public void testHasFrequency() throws IOException {
 	
 	@Test
 	public void testTabDelimitedGLStringFile() {
-		LinkedHashMap<String, String> glStrings = GLStringUtilities.readGLStringFile("tabDelimitedExample.txt");
-		for (String key : glStrings.keySet()) {
-			assertTrue(TAB_DELIMITED.equals(key));
+		List<LinkageDisequilibriumGenotypeList> glStrings = GLStringUtilities.readGLStringFile("tabDelimitedExample.txt");
+		for (LinkageDisequilibriumGenotypeList linkedGLString : glStrings) {
+			assertTrue(TAB_DELIMITED.equals(linkedGLString.getId()));
+			assertTrue(MY_NOTE.equals(linkedGLString.getNote()));
 		}
 	}
 	
 	@Test
 	public void testCommaDelimitedGLStringFile() {
-		LinkedHashMap<String, String> glStrings = GLStringUtilities.readGLStringFile("commaDelimitedExample.txt");
-		for (String key : glStrings.keySet()) {
-			assertTrue(COMMA_DELIMITED.equals(key));
+		List<LinkageDisequilibriumGenotypeList> glStrings = GLStringUtilities.readGLStringFile("commaDelimitedExample.txt");
+		for (LinkageDisequilibriumGenotypeList linkedGLString : glStrings) {
+			assertTrue(COMMA_DELIMITED.equals(linkedGLString.getId()));
 		}
 	}
 	
 	@Test
 	public void testHMLFile() {
-		LinkedHashMap<String, String> glStrings = GLStringUtilities.readGLStringFile("hml_1_0_2-example7-ngsFull.xml");
-		for (String key : glStrings.keySet()) {
-			assertTrue("1367-7150-8".equals(key));
+		List<LinkageDisequilibriumGenotypeList> glStrings = GLStringUtilities.readGLStringFile("hml_1_0_2-example7-ngsFull.xml");
+		for (LinkageDisequilibriumGenotypeList linkedGLString : glStrings) {
+			assertTrue("1367-7150-8".equals(linkedGLString.getId()));
 		}	
 	}
 	
diff --git a/ld-validation/src/test/resources/tabDelimitedExample.txt b/ld-validation/src/test/resources/tabDelimitedExample.txt
index ae84985..51c0fbd 100644
--- a/ld-validation/src/test/resources/tabDelimitedExample.txt
+++ b/ld-validation/src/test/resources/tabDelimitedExample.txt
@@ -1 +1 @@
-TAB_DELIMITED	HLA-A*01:01:01:01+HLA-A*26:01:01^HLA-B*38:01:01/HLA-B*38:27+HLA-B*44:03:01/HLA-B*44:03:10/HLA-B*44:125^HLA-C*04:01:01:01/HLA-C*04:01:01:02/HLA-C*04:01:01:03/HLA-C*04:01:01:04/HLA-C*04:01:01:05/HLA-C*04:20/HLA-C*04:117+HLA-C*12:03:01:01/HLA-C*12:03:01:02/HLA-C*12:34^HLA-DPA1*01:03:01:01/HLA-DPA1*01:03:01:02/HLA-DPA1*01:03:01:03/HLA-DPA1*01:03:01:04/HLA-DPA1*01:03:01:05+HLA-DPA1*01:03:01:01/HLA-DPA1*01:03:01:02/HLA-DPA1*01:03:01:03/HLA-DPA1*01:03:01:04/HLA-DPA1*01:03:01:05^HLA-DPB1*04:01:01:01/HLA-DPB1*04:01:01:02+HLA-DPB1*04:01:01:01/HLA-DPB1*04:01:01:02^HLA-DQA1*02:01+HLA-DQA1*05:05:01:01/HLA-DQA1*05:05:01:02/HLA-DQA1*05:05:01:03/HLA-DQA1*05:09/HLA-DQA1*05:11^HLA-DQB1*02:02+HLA-DQB1*03:01:01:01/HLA-DQB1*03:01:01:02/HLA-DQB1*03:01:01:03^HLA-DRB1*07:01:01:01/HLA-DRB1*07:01:01:02+HLA-DRB1*11:01:01^HLA-DRB3*02:02:01:01/HLA-DRB3*02:02:01:02^HLA-DRB4*01:01:01:01/HLA-DRB4*03:01N
\ No newline at end of file
+TAB_DELIMITED	HLA-A*01:01:01:01+HLA-A*26:01:01^HLA-B*38:01:01/HLA-B*38:27+HLA-B*44:03:01/HLA-B*44:03:10/HLA-B*44:125^HLA-C*04:01:01:01/HLA-C*04:01:01:02/HLA-C*04:01:01:03/HLA-C*04:01:01:04/HLA-C*04:01:01:05/HLA-C*04:20/HLA-C*04:117+HLA-C*12:03:01:01/HLA-C*12:03:01:02/HLA-C*12:34^HLA-DPA1*01:03:01:01/HLA-DPA1*01:03:01:02/HLA-DPA1*01:03:01:03/HLA-DPA1*01:03:01:04/HLA-DPA1*01:03:01:05+HLA-DPA1*01:03:01:01/HLA-DPA1*01:03:01:02/HLA-DPA1*01:03:01:03/HLA-DPA1*01:03:01:04/HLA-DPA1*01:03:01:05^HLA-DPB1*04:01:01:01/HLA-DPB1*04:01:01:02+HLA-DPB1*04:01:01:01/HLA-DPB1*04:01:01:02^HLA-DQA1*02:01+HLA-DQA1*05:05:01:01/HLA-DQA1*05:05:01:02/HLA-DQA1*05:05:01:03/HLA-DQA1*05:09/HLA-DQA1*05:11^HLA-DQB1*02:02+HLA-DQB1*03:01:01:01/HLA-DQB1*03:01:01:02/HLA-DQB1*03:01:01:03^HLA-DRB1*07:01:01:01/HLA-DRB1*07:01:01:02+HLA-DRB1*11:01:01^HLA-DRB3*02:02:01:01/HLA-DRB3*02:02:01:02^HLA-DRB4*01:01:01:01/HLA-DRB4*03:01N	My Note
\ No newline at end of file