diff --git a/gortools/src/main/scala/gorsat/Analysis/GtGenAnalysis.scala b/gortools/src/main/scala/gorsat/Analysis/GtGenAnalysis.scala
index c61b02ee5..861de4237 100644
--- a/gortools/src/main/scala/gorsat/Analysis/GtGenAnalysis.scala
+++ b/gortools/src/main/scala/gorsat/Analysis/GtGenAnalysis.scala
@@ -61,7 +61,7 @@ object GtGenAnalysis {
         sh.buckValueCols(i).setLength(buckSize)
         var j = 0
         while (j < buckSize) {
-          sh.buckValueCols(i).setCharAt(j, '3') // Missing
+          sh.buckValueCols(i).setCharAt(j, '#') // Missing
           j += 1
         }
         i += 1
@@ -180,7 +180,7 @@ object GtGenAnalysis {
     if (!useGroup) groupMap += (-1 -> singleGroupHolder)
 
     def set_coverage(lSeg: CovSEGinfo, rSeg: CovSEGinfo): Unit = {
-      if (lSeg.values.charAt(rSeg.buckPos) =='4') lSeg.values.setCharAt(rSeg.buckPos, '0')
+      if (lSeg.values.charAt(rSeg.buckPos) =='#') lSeg.values.setCharAt(rSeg.buckPos, '0')
     }
 
     def nested_process(lr: Row, next_lr: Row): Unit = {
@@ -291,7 +291,7 @@ object GtGenAnalysis {
       }
 
       //#######
-      super.process(RowObj(s"${lr.colsSlice(0, bucketCol+1)}\t${lSeg.values.toString() }"))
+      super.process(RowObj(s"${lr.colsSlice(0, bucketCol+1)}\t${lSeg.values.toString().replace('#','3') }"))
 
       if ((lr.chr == lastLeftChr && maxLeftStop < leftStop) || lr.chr != lastLeftChr) maxLeftStop = leftStop
       lastLeftChr = lr.chr
diff --git a/gortools/src/test/java/gorsat/gtgen/UTestGTGen.java b/gortools/src/test/java/gorsat/gtgen/UTestGTGen.java
index d6505c15d..98e867649 100644
--- a/gortools/src/test/java/gorsat/gtgen/UTestGTGen.java
+++ b/gortools/src/test/java/gorsat/gtgen/UTestGTGen.java
@@ -1,5 +1,6 @@
 package gorsat.gtgen;
 
+import gorsat.TestUtils;
 import org.junit.Assert;
 import org.junit.Test;
 
@@ -232,4 +233,18 @@ public void test_getAn() {
         gtGen.setPrior(0.01, 1000);
         Assert.assertEquals(1001, gtGen.getAn());
     }
+
+    @Test
+    public void testGTGENunknown() {
+        TestUtils.runGorPipe("""
+             create #vars# = gorrow chr1,1 | calc ref 'A,A' | calc alt 'C,C' | calc GT '1,1' | calc pn 'pn1,pn2' | split ref,alt,gt,pn;
+             create #goodcov# = gorrow chr1,0,3 | calc pn 'pn1,pn2' | split pn;
+             create #bucket# = nor [#vars#] | select pn | calc bucket 'b1';
+             
+             gor [#vars#] | gtgen -gc ref,alt [#bucket#] [#goodcov#] | throwif values != '11'
+             | merge <(gor [#vars#] | where pn != 'pn2' | gtgen -gc ref,alt [#bucket#] [#goodcov#] | throwif values != '10')
+             | merge <(gor [#vars#] | where pn != 'pn2' | gtgen -gc ref,alt [#bucket#] <(gor [#goodcov#] | where pn != 'pn2') | throwif values != '13')
+           """ );
+    }
+
 }