diff --git a/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java b/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
index 41e20e907..5c303594a 100644
--- a/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
+++ b/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
@@ -3,7 +3,7 @@
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -81,7 +81,7 @@ public static String getLastHeaderLine(List<String> headerLines) {
 	 * return an empty map if any of the fields are not in the header
 	 */
 	public static Map<String, Integer> getHeaderNameAndPositions(String fieldNames, String header) {
-		Map<String, Integer> namePositions = new HashMap<>();
+		Map<String, Integer> namePositions = new LinkedHashMap<>();
 		
 		System.out.println("header: " + header);
 		
diff --git a/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotateTest.java b/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotateTest.java
index 96b4c666c..a032392cb 100644
--- a/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotateTest.java
+++ b/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotateTest.java
@@ -115,7 +115,7 @@ public void jsonInputsTSV() throws IOException {
 		AnnotateUtils.populateAnnotationSources(ais, sources);
 		assertEquals(1, sources.size());
 		String annotation = sources.getFirst().getAnnotation(ChrPositionUtils.convertContigAndPositionToLong("1", 655652), new ChrPositionRefAlt("chr1", 655652, 655652, "A", "T"));
-		assertEquals("HGVSc_VEP=c.1A>C\tHGVSp_VEP=p.Met1?\taaref=M", annotation);
+		assertEquals("aaref=M\tHGVSc_VEP=c.1A>C\tHGVSp_VEP=p.Met1?", annotation);
 	}
 	
 	@Test