--- bismark	2012-10-09 10:45:47.758418637 +0200
+++ bismark.modif	2012-10-10 13:04:28.192505594 +0200
@@ -5832,8 +5832,11 @@
 
   #####
 
+  ### XA = single end non-BS-mismatch rate
+  my $XA_tag = "XA:Z:$number_of_mismatches";
+
   # SAM format: QNAME, FLAG, RNAME, 1-based POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN, SEQ, QUAL, optional fields
-  print OUT join("\t",($id,$flag,$chr,$start,$mapq,$cigar,$rnext,$pnext,$tlen,$actual_seq,$qual,$NM_tag,$XX_tag,$XM_tag,$XR_tag,$XG_tag)),"\n";
+  print OUT join("\t",($id,$flag,$chr,$start,$mapq,$cigar,$rnext,$pnext,$tlen,$actual_seq,$qual,$NM_tag,$XX_tag,$XM_tag,$XR_tag,$XG_tag,$XA_tag)),"\n";
 }
 
 
@@ -6168,11 +6171,14 @@
 
   my $XG_tag = "XG:Z:$genome_conversion";                              # Optional tag XG: Genome Conversion state; valid for both reads
 
-  #####
+  ### XA = paired end mate 1 non-BS mismatch rate
+  ### XB = paired end mate 2 non-BS mismatch rate
+  my $XA_tag = "XA:Z:$number_of_mismatches_1";
+  my $XB_tag = "XB:Z:$number_of_mismatches_2";
 
   # SAM format: QNAME, FLAG, RNAME, 1-based POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN, SEQ, QUAL, optional fields
-  print OUT join("\t", ($id_1, $flag_1, $chr, $start_read_1, $mapq, $cigar_1, $rnext, $pnext_1, $tlen_1, $actual_seq_1, $qual_1, $NM_tag_1, $XX_tag_1, $XM_tag_1,$XR_tag_1,$XG_tag)), "\n";
-  print OUT join("\t", ($id_2, $flag_2, $chr, $start_read_2, $mapq, $cigar_2, $rnext, $pnext_2, $tlen_2, $actual_seq_2, $qual_2, $NM_tag_2, $XX_tag_2, $XM_tag_2,$XR_tag_2,$XG_tag)), "\n";
+  print OUT join("\t", ($id_1, $flag_1, $chr, $start_read_1, $mapq, $cigar_1, $rnext, $pnext_1, $tlen_1, $actual_seq_1, $qual_1, $NM_tag_1, $XX_tag_1, $XM_tag_1,$XR_tag_1,$XG_tag,$XA_tag)), "\n";
+  print OUT join("\t", ($id_2, $flag_2, $chr, $start_read_2, $mapq, $cigar_2, $rnext, $pnext_2, $tlen_2, $actual_seq_2, $qual_2, $NM_tag_2, $XX_tag_2, $XM_tag_2,$XR_tag_2,$XG_tag,$XB_tag)), "\n";
 }
 
 sub revcomp{