Index: src/hg/hgTracks/cds.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/cds.c,v
retrieving revision 1.100
retrieving revision 1.101
diff -b -B -U 4 -r1.100 -r1.101
--- src/hg/hgTracks/cds.c	10 Jun 2009 19:46:20 -0000	1.100
+++ src/hg/hgTracks/cds.c	24 Jun 2009 22:32:24 -0000	1.101
@@ -303,9 +303,9 @@
 	int mrnaS = -1;
 	if (psl)
 	    mrnaS = convertCoordUsingPsl(s, psl);
 	else
-	    mrnaS = sf->qStart;
+	    mrnaS = sf->qStart + (s - sf->start);
 	if(mrnaS >= 0)
 	    {
 	    int i;
 	    for (i=0; i < (e - s); i++)

