diff --git a/bin/agat_sp_compare_two_annotations.pl b/bin/agat_sp_compare_two_annotations.pl
index 30ee0228..99ca41db 100755
--- a/bin/agat_sp_compare_two_annotations.pl
+++ b/bin/agat_sp_compare_two_annotations.pl
@@ -54,9 +54,22 @@
 # --- Manage config ---
 $config = get_agat_config({config_file_in => $config});
 
+######################
+# Manage output folder #
+
+if (! $opt_output) {
+  print "Default output name: split_result\n";
+  $opt_output="comparison_result";
+}
+
+if (-d $opt_output){
+  print "The output directory choosen already exists. Please give me another Name.\n";exit();
+}
+mkdir $opt_output;
+
 ######################
 # Manage output file #
-my $report = prepare_fileout($opt_output);
+my $report = prepare_fileout("$opt_output/report.txt");
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     MAIN     <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -323,7 +336,9 @@
 									my $flat_overlap_1 = $locations1;
 									my $flat_overlap_2 = $locations2;
 									my $overlap_A=1;
+									my @overlap_A_id=($locations1->[0][3]);
 									my $overlap_B=1;
+									my @overlap_B_id=($locations2->[0][3]);
 									my $loop="top";
 									my $flip=2;
 									my $current_locs;
@@ -372,9 +387,11 @@
 
 												if($loop eq "top"){
 													$overlap_A++;
+													push @overlap_A_id, $locations->[0][3];
 												}
 												elsif($loop eq "bot"){
 													$overlap_B++;
+													push @overlap_B_id, $locations->[0][3];
 												}
 											}
 											else{
@@ -398,14 +415,14 @@
 											}
 										}
 									}
-									$overlap_info{$locations1->[0][2]}{$overlap_A}{$overlap_B}++;
+									push @{$overlap_info{$locations1->[0][2]}{$overlap_A}{$overlap_B}}, [ [@overlap_A_id], [@overlap_B_id] ];
 								}
 		# ----------------------------------- CASE 1 -----------------------------------
 								#  location A                         ----------------
 								#  location B  ---------------
 								elsif ($locations2->[scalar(@{$locations2})-1][1] < $locations1->[0][0] ){
 
-									$overlap_info{$locations1->[0][2]}{0}{1}++;
+									push @{$overlap_info{$locations1->[0][2]}{0}{1}}, [[undef], [$locations2->[0][3]]];
 									print "Case1 notoverlap !\n\n" if ($debug);
 									# throw loc2
 									remove_loc_by_id($flattened_locations2_clean_sorted, $locusID, $chimere_type, $locations2->[0][3]);
@@ -420,7 +437,7 @@
 									my $id1 = $locations1->[0][3];
 									print "Case2 notoverlap !\n" if ($debug);
 									if(! exists_keys(\%seen1, ( $id1 ) ) ){ # else it has been dealed by overlap case
-										$overlap_info{$locations1->[0][2]}{1}{0}++;
+										push @{$overlap_info{$locations1->[0][2]}{1}{0}}, [ [$locations1->[0][3]], [undef] ];
 										# throw loc1
 										remove_loc_by_id($flattened_locations1_clean_sorted, $locusID, $chimere_type, $id1);
 										$seen1{$id1}++;
@@ -442,7 +459,7 @@
 foreach my $locusID (  keys %{$flattened_locations1_clean_sorted} ){
   foreach my $chimere_type ( keys %{$flattened_locations1_clean_sorted->{$locusID}}){
     foreach my $locations1 ( @{$flattened_locations1_clean_sorted->{$locusID}{$chimere_type}} ){
-			$overlap_info{$locations1->[0][2]}{1}{0}++;
+			push @{$overlap_info{$locations1->[0][2]}{1}{0}}, [ [$locations1->[0][3]], [undef]];
 			print " Case3 !\n" if ($debug);
     }
   }
@@ -454,7 +471,7 @@
 foreach my $locusID (  keys %{$flattened_locations2_clean_sorted} ){
   foreach my $chimere_type ( keys %{$flattened_locations2_clean_sorted->{$locusID}}){
     foreach my $locations2 ( @{$flattened_locations2_clean_sorted->{$locusID}{$chimere_type}} ){
-			$overlap_info{$locations2->[0][2]}{0}{1}++;
+			push @{$overlap_info{$locations2->[0][2]}{0}{1}},  [ [undef], [$locations2->[0][3]] ];
 			print " Case4 !\n" if ($debug);
     }
   }
@@ -491,12 +508,50 @@
 		$total{$type_l1}{'B'}=0;
     foreach my $value1 ( sort {$a <=> $b} keys %{$overlap_info{$type_l1}} ){
       foreach my $value2 ( sort {$a <=> $b}  keys %{$overlap_info{$type_l1}{$value1}} ){
-        $string_to_print .= "|".sizedPrint($value1,30)."|".sizedPrint($value2,30)."|".sizedPrint($overlap_info{$type_l1}{$value1}{$value2},30)."|\n";
-        if ($value1 != 0){
-          $total{$type_l1}{'A'} += $value1 * $overlap_info{$type_l1}{$value1}{$value2};
+        $string_to_print .= "|".sizedPrint($value1,30)."|".sizedPrint($value2,30)."|".sizedPrint(scalar(@{$overlap_info{$type_l1}{$value1}{$value2}}),30)."|\n";
+        
+		# report ids
+		my $report_ids = prepare_fileout("$opt_output/$value1"."_".$value2."_id_list.txt");
+		# file1
+		foreach my $array ( @{$overlap_info{$type_l1}{$value1}{$value2}}) {
+			my $cpt=0;
+			my $last = scalar(@{$array->[0]});
+			foreach my $value ( @{$array->[0]} ) { # array0 is id overlarpA
+				$cpt++;
+				if(! $value){
+					print $report_ids "-";
+				} else {
+					if ($last == $cpt){
+						print $report_ids $value;
+					} else {
+						print $report_ids $value.", ";
+					}
+				}
+			}
+			print $report_ids " | ";
+			my $cpt2=0;
+			my $last2 = scalar(@{$array->[1]});
+			foreach my $value ( @{$array->[1]} ) { # array1 is id overlarpB
+				$cpt2++;
+				if(! $value){
+					print $report_ids "-\n";
+				} else {
+					if ($last2 == $cpt2){
+						print $report_ids "$value"
+					} else {
+						print $report_ids "$value, "
+					}
+				}
+			}
+			print $report_ids "\n";
+		}
+
+
+		if ($value1 != 0){
+          $total{$type_l1}{'A'} += $value1 * scalar(@{$overlap_info{$type_l1}{$value1}{$value2}});
         }
         if ($value2 != 0){
-          $total{$type_l1}{'B'} += $value2 * $overlap_info{$type_l1}{$value1}{$value2};
+          $total{$type_l1}{'B'} += $value2 * scalar(@{$overlap_info{$type_l1}{$value1}{$value2}});
         }
       }
     }