--- a/wrapper.sh	Tue May 24 03:59:44 2016 -0400
+++ b/wrapper.sh	Thu May 26 08:18:13 2016 -0400
@@ -90,10 +90,6 @@
 echo "R mutation analysis"
 Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1
 
-#echo "." > $output
-#exit 0
-
-
 
 echo "---------------- mutation_analysis.py ----------------"
 echo "---------------- mutation_analysis.py ----------------<br />" >> $output
@@ -119,7 +115,7 @@
 
 while read ID class seq A C G T
 do
-	echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
+	echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
 done < $outdir/sequence_overview/ntoverview.txt