diff --git a/bin/agat b/bin/agat
index b87924fd..8151ac26 100755
--- a/bin/agat
+++ b/bin/agat
@@ -193,6 +193,10 @@ force_gff_input_version, gtf_output_version, gff_output_version and output_forma
 							getopt      => 'gtf_output_version=s',
 							help        => 'Set the GTF output vesion. Choice 1, 2, 2.1, 2.2, 2.5, 3 or relax. [Default relax]',
 					 },
+					{
+							getopt      => 'deflate_attribute!',
+							help        => 'deflate multi-values attributes:  attribute_tag=att_value1,att_value2,att_value3 will will become attribute_tag=att_value1;attribute_tag2=att_value2;attribute_tag3=att_value3;',
+					 },
 					 {
 							getopt      => 'create_l3_for_l2_orphan!',
 							help        => 'To create l3 feature for l2 feature without any. [Default activated]',
diff --git a/lib/AGAT/AGAT.pm b/lib/AGAT/AGAT.pm
index a9885f37..e5859e79 100644
--- a/lib/AGAT/AGAT.pm
+++ b/lib/AGAT/AGAT.pm
@@ -17,8 +17,9 @@ use AGAT::PlotR;
 use Bio::Tools::GFF;
 
 our $VERSION     = "v1.4.1";
-our @ISA         = qw(Exporter);
-our @EXPORT      = qw(get_agat_header print_agat_version get_agat_config handle_levels);
+our $CONFIG; # This variable will be used to store the config and will be available from everywhere.
+our @ISA         = qw( Exporter );
+our @EXPORT      = qw( get_agat_header print_agat_version get_agat_config handle_levels );
 sub import {
     AGAT::AGAT->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
     AGAT::OmniscientI->export_to_level(1, @_);
@@ -159,6 +160,10 @@ sub get_agat_config{
 	# Load the config
 	my $config = load_config({ config_file => $config_file_checked});
 	check_config({ config => $config});
+
+	# Store the config in a Global variable accessible from everywhere.
+	$CONFIG = $config;
+	
 	return $config;
 }
 
@@ -243,6 +248,7 @@ sub handle_config {
 		my $output_format = $general->{configs}[-1]{output_format};
 		my $gff_output_version = $general->{configs}[-1]{gff_output_version};
 		my $gtf_output_version = $general->{configs}[-1]{gtf_output_version};
+		my $deflate_attribute = $general->{configs}[-1]{deflate_attribute};
 		my $create_l3_for_l2_orphan = $general->{configs}[-1]{create_l3_for_l2_orphan};
 		my $clean_attributes_from_template = $general->{configs}[-1]{clean_attributes_from_template};
 		my $locus_tag = $general->{configs}[-1]{locus_tag};
@@ -325,6 +331,11 @@ sub handle_config {
 				$modified_on_the_fly = 1;
 			}
 			# bolean
+			if( defined($deflate_attribute) ){
+				$config->{ deflate_attribute } = _make_bolean($deflate_attribute);
+				$modified_on_the_fly = 1;
+			}
+			# bolean
 			if( defined($create_l3_for_l2_orphan) ){
 				$config->{ create_l3_for_l2_orphan } = _make_bolean($create_l3_for_l2_orphan);
 				$modified_on_the_fly = 1;
diff --git a/lib/AGAT/BioperlGFF.pm b/lib/AGAT/BioperlGFF.pm
index 1dda601e..bc5d6a2c 100644
--- a/lib/AGAT/BioperlGFF.pm
+++ b/lib/AGAT/BioperlGFF.pm
@@ -149,6 +149,8 @@ package AGAT::BioperlGFF;
 use vars qw($HAS_HTML_ENTITIES);
 use strict;
 
+use AGAT::OmniscientTool;
+use AGAT::AGAT;
 use Bio::Seq::SeqFactory;
 use Bio::LocatableSeq;
 use Bio::SeqFeature::Generic;
@@ -699,6 +701,28 @@ sub write_feature {
         $self->_print($line);
     }
     $self->{'_first'} = 0;
+
+    # deflate multi-values attribute if asked by config
+    if ($AGAT::AGAT::CONFIG->{'deflate_attribute'}){
+        foreach my $feature ( @features ) {
+            my @list_tags= $feature->get_all_tags();
+			foreach my $tag (@list_tags){
+				my @tag_values = $feature->get_tag_values($tag);
+                if ($#tag_values >= 1){
+                    my $tag_counter=-1;
+					foreach my $tag_value (@tag_values){
+                        $tag_counter++;
+                        if ($tag_counter == 0){
+                            create_or_replace_tag($feature, $tag , $tag_value);
+                        } else {
+                            create_or_replace_tag($feature, $tag."_".$tag_counter , $tag_value);
+                        }	
+					}
+				}
+			}
+        }
+    }
+
     foreach my $feature ( @features ) {
         $self->_print($self->gxf_string($feature)."\n");
     }
diff --git a/lib/AGAT/Config.pm b/lib/AGAT/Config.pm
index dc422ae4..d1ca76e8 100644
--- a/lib/AGAT/Config.pm
+++ b/lib/AGAT/Config.pm
@@ -175,7 +175,7 @@ sub check_config{
 		$error = 1;
 	}
 	if( !  exists_keys($config,("log") ) ){
-		print "progress_bar parameter missing in the configuration file.\n";
+		print "log parameter missing in the configuration file.\n";
 		$error = 1;
 	}
 	if( !  exists_keys($config, ("debug") ) ){
@@ -241,6 +241,10 @@ sub check_config{
 		print "gtf_output_version parameter missing in the configuration file.\n";
 		$error = 1;
 	}
+	if( ! exists_keys($config, ("deflate_attribute") ) ) {
+		print "deflate_attribute parameter missing in the configuration file.\n";
+		$error = 1;
+	}
 	if( ! exists_keys($config, ("create_l3_for_l2_orphan") ) ) {
 		print "create_level3_for_level2_orphan parameter missing in the configuration file.\n";
 		$error = 1;
diff --git a/lib/AGAT/OmniscientToGTF.pm b/lib/AGAT/OmniscientToGTF.pm
index 45470c0a..ef1e60cd 100644
--- a/lib/AGAT/OmniscientToGTF.pm
+++ b/lib/AGAT/OmniscientToGTF.pm
@@ -66,169 +66,166 @@ sub print_omniscient_as_gtf{
 				print "\n\n\nlevel1: ".$feature_level1->gff_string."\n" if $debug;
 				my $id_tag_key_level1 = lc($feature_level1->_tag_value('ID'));
 
-	      # Gene ID level1
+				# Gene ID level1
 				my $gene_id=undef;
-	      my $gene_id_att=undef;
-	      if($feature_level1->has_tag('gene_id')){
-	        $gene_id_att=$feature_level1->_tag_value('gene_id');
-	      }
-
-	      my $transcript_id=undef;
-	      my $level3_gene_id=undef;
-	      #################
-	      # == LEVEL 2 == #
-	      #################
-	      foreach my $primary_tag_key_level2 ( sort {$a cmp $b} keys %{$hash_omniscient->{'level2'}}){ # primary_tag_key_level2 = mrna or mirna or ncrna or trna etc...
-
-	        if ( exists_keys ($hash_omniscient, ('level2', $primary_tag_key_level2, $id_tag_key_level1) ) ){
-	          foreach my $feature_level2 ( sort {$a->start <=> $b->start} @{$hash_omniscient->{'level2'}{$primary_tag_key_level2}{$id_tag_key_level1}}) {
+				my $gene_id_att=undef;
+				if($feature_level1->has_tag('gene_id')){
+					$gene_id_att=$feature_level1->_tag_value('gene_id');
+				}
+
+	      		my $transcript_id=undef;
+	      		my $level3_gene_id=undef;
+				#################
+				# == LEVEL 2 == #
+				#################
+				foreach my $primary_tag_key_level2 ( sort {$a cmp $b} keys %{$hash_omniscient->{'level2'}}){ # primary_tag_key_level2 = mrna or mirna or ncrna or trna etc...
+
+					if ( exists_keys ($hash_omniscient, ('level2', $primary_tag_key_level2, $id_tag_key_level1) ) ){
+						foreach my $feature_level2 ( sort {$a->start <=> $b->start} @{$hash_omniscient->{'level2'}{$primary_tag_key_level2}{$id_tag_key_level1}}) {
 							print "\nlevel2: ".$feature_level2->gff_string."\n" if $debug;
 
+							# Gene ID level2
+							my $gene_id_mrna_att=undef;
+							if($feature_level2->has_tag('gene_id')){
+								$gene_id_mrna_att=$feature_level2->_tag_value('gene_id');
+							}
 
-	            # Gene ID level2
-	            my $gene_id_mrna_att=undef;
-	            if($feature_level2->has_tag('gene_id')){
-	              $gene_id_mrna_att=$feature_level2->_tag_value('gene_id');
-	            }
+							my $transcript_id_mrna_att=undef;
+							if($feature_level2->has_tag('transcript_id')){
+								$transcript_id_mrna_att=$feature_level2->_tag_value('transcript_id');
+							}
+
+							# get gff3 feature (ID)
+							my $level2_ID = lc($feature_level2->_tag_value('ID'));
+							my $level3_transcript_id=undef;
+							#################
+							# == LEVEL 3 == #
+							#################
+
+							############
+							# Go through one time to check if gene_id and transcript_id are present and save them
+							foreach my $primary_tag_key_level3 ( sort {$a cmp $b} keys %{$hash_omniscient->{'level3'}}){ # primary_tag_key_level3 = cds or exon or start_codon or utr etc...
+								if ( exists_keys ($hash_omniscient, ('level3', $primary_tag_key_level3, $level2_ID) ) ){
+									foreach my $feature_level3 ( sort { $a->start <=> $b->start } @{$hash_omniscient->{'level3'}{$primary_tag_key_level3}{$level2_ID}}) {
+										print "level3: ".$feature_level3->gff_string."\n" if $debug;
+										#Get level3 gene_id
+										if(! $level3_gene_id){
+											if($feature_level3->has_tag('gene_id')){
+												$level3_gene_id=$feature_level3->_tag_value('gene_id');
+											}
+										}
+
+										#Get level3 transcript_id
+										if(! $level3_transcript_id){
+											if($feature_level3->has_tag('transcript_id')){
+												$level3_transcript_id=$feature_level3->_tag_value('transcript_id');
+											}
+										}
+										if($level3_gene_id and $level3_transcript_id){last;}
+									}
+								}
+								if($level3_gene_id and $level3_transcript_id){last;}
+							}
 
-	            my $transcript_id_mrna_att=undef;
-	            if($feature_level2->has_tag('transcript_id')){
-	              $transcript_id_mrna_att=$feature_level2->_tag_value('transcript_id');
-	            }
+							#################
+							# CHOOSE the gene_id. We take the first from level1 to level3.
+							if($gene_id_att and ! _does_id_exist("gene_id", $gene_id_att, \%keep_track_gene_id) ){
+								$gene_id=$gene_id_att;
+							}
+							elsif($gene_id_mrna_att and ! _does_id_exist("gene_id", $gene_id_mrna_att, \%keep_track_gene_id) ){
+								$gene_id=$gene_id_mrna_att
+							}
+							elsif($level3_gene_id and ! _does_id_exist("gene_id", $level3_gene_id, \%keep_track_gene_id) ){
+								$gene_id=$level3_gene_id;
+							}
+							else{ # We didn't find any gene_id we will the ID of level1 as gene_id.
+								$gene_id=$feature_level1->_tag_value('ID');
+							}
 
-	            # get gff3 feature (ID)
-	            my $level2_ID = lc($feature_level2->_tag_value('ID'));
+							#################
+							# CHOOSE the transcript_id. We take the first from level2 to level3.
+							if($transcript_id_mrna_att and ! _does_id_exist("transcript_id", $transcript_id_mrna_att, \%keep_track_transcript_id) ){
+								$transcript_id=$transcript_id_mrna_att;
+							}
+							elsif($level3_transcript_id and ! _does_id_exist("transcript_id", $level3_transcript_id, \%keep_track_transcript_id) ){
+								$transcript_id=$level3_transcript_id;
+							}
+							else{ # We didn't find any gene_id we will the ID of level2 as transcript_id.
+								$transcript_id=$feature_level2->_tag_value('ID');
+							}
 
-	            my $level3_transcript_id=undef;
-	            #################
-	            # == LEVEL 3 == #
-	            #################
+							##############
+							# Second pass of level3 features
+							# Add gene_id and transcript_id to level3 feature that don't have this information
+							foreach my $primary_tag_key_level3 (keys %{$hash_omniscient->{'level3'}}){ # primary_tag_key_level3 = cds or exon or start_codon or utr etc...
+								if ( exists_keys ($hash_omniscient, ('level3', $primary_tag_key_level3, $level2_ID) ) ){
+									foreach my $feature_level3 ( @{$hash_omniscient->{'level3'}{$primary_tag_key_level3}{$level2_ID}}) {
 
-	            ############
-	            # Go through one time to check if gene_id and transcript_id are present and save them
-	            foreach my $primary_tag_key_level3 ( sort {$a cmp $b} keys %{$hash_omniscient->{'level3'}}){ # primary_tag_key_level3 = cds or exon or start_codon or utr etc...
-	              if ( exists_keys ($hash_omniscient, ('level3', $primary_tag_key_level3, $level2_ID) ) ){
-	                foreach my $feature_level3 ( sort { $a->start <=> $b->start } @{$hash_omniscient->{'level3'}{$primary_tag_key_level3}{$level2_ID}}) {
-										print "level3: ".$feature_level3->gff_string."\n" if $debug;
-	                  #Get level3 gene_id
-	                  if(! $level3_gene_id){
-	                    if($feature_level3->has_tag('gene_id')){
-	                      $level3_gene_id=$feature_level3->_tag_value('gene_id');
-	                    }
-	                  }
-
-	                  #Get level3 transcript_id
-	                  if(! $level3_transcript_id){
-	                    if($feature_level3->has_tag('transcript_id')){
-	                      $level3_transcript_id=$feature_level3->_tag_value('transcript_id');
-	                    }
-	                  }
-	                  if($level3_gene_id and $level3_transcript_id){last;}
-	                }
-	              }
-	              if($level3_gene_id and $level3_transcript_id){last;}
-	            }
-
-	            #################
-	            # CHOOSE the gene_id. We take the first from level1 to level3.
-	            if($gene_id_att and ! _does_id_exist("gene_id", $gene_id_att, \%keep_track_gene_id) ){
-	              $gene_id=$gene_id_att;
-	            }
-	            elsif($gene_id_mrna_att and ! _does_id_exist("gene_id", $gene_id_mrna_att, \%keep_track_gene_id) ){
-	              $gene_id=$gene_id_mrna_att
-	            }
-	            elsif($level3_gene_id and ! _does_id_exist("gene_id", $level3_gene_id, \%keep_track_gene_id) ){
-	              $gene_id=$level3_gene_id;
-	            }
-	            else{ # We didn't find any gene_id we will the ID of level1 as gene_id.
-	              $gene_id=$feature_level1->_tag_value('ID');
-	            }
-
-	            #################
-	            # CHOOSE the transcript_id. We take the first from level2 to level3.
-	            if($transcript_id_mrna_att and ! _does_id_exist("transcript_id", $transcript_id_mrna_att, \%keep_track_transcript_id) ){
-	              $transcript_id=$transcript_id_mrna_att;
-	            }
-	            elsif($level3_transcript_id and ! _does_id_exist("transcript_id", $level3_transcript_id, \%keep_track_transcript_id) ){
-	              $transcript_id=$level3_transcript_id;
-	            }
-	            else{ # We didn't find any gene_id we will the ID of level2 as transcript_id.
-	              $transcript_id=$feature_level2->_tag_value('ID');
-	            }
-
-	            ##############
-	            # Second pass of level3 features
-	            # Add gene_id and transcript_id to level3 feature that don't have this information
-	            foreach my $primary_tag_key_level3 (keys %{$hash_omniscient->{'level3'}}){ # primary_tag_key_level3 = cds or exon or start_codon or utr etc...
-	              if ( exists_keys ($hash_omniscient, ('level3', $primary_tag_key_level3, $level2_ID) ) ){
-	                foreach my $feature_level3 ( @{$hash_omniscient->{'level3'}{$primary_tag_key_level3}{$level2_ID}}) {
-
-	                  #Check add gene_id
-	                  if(! $feature_level3->has_tag('gene_id')) {
-	                    $feature_level3->add_tag_value('gene_id', $gene_id);
-	                  }
-	                  elsif($feature_level3->_tag_value('gene_id') ne $gene_id) { #gene_id different, we replace it.
-	                    warn("Level3 ".$feature_level3->_tag_value('ID').": We replace the gene_id ".$feature_level3->_tag_value('gene_id')." by ".$gene_id.". We save original gene_id into $previous_tag_l1 attribute.\n");
-											create_or_replace_tag($feature_level3, $previous_tag_l1, $feature_level3->_tag_value('gene_id'));
-											create_or_replace_tag($feature_level3, 'gene_id', $gene_id);
-	                  }
-	                  #Check add transcript_id
-	                  if(! $feature_level3->has_tag('transcript_id')){
-	                    $feature_level3->add_tag_value('transcript_id', $transcript_id);
-	                  }
-	                  elsif($feature_level3->_tag_value('transcript_id') ne $transcript_id){ #transcript_id different, we replace it.
-	                    warn("Level3 ".$feature_level3->_tag_value('ID').": We replace the transcript_id ".$feature_level3->_tag_value('transcript_id')." by ".$transcript_id.". We save original transcript_id into $previous_tag_l2 attribute.\n");
-										  create_or_replace_tag($feature_level3, $previous_tag_l2, $feature_level3->_tag_value('transcript_id'));
+										#Check add gene_id
+										if(! $feature_level3->has_tag('gene_id')) {
+											$feature_level3->add_tag_value('gene_id', $gene_id);
+										}
+										elsif($feature_level3->_tag_value('gene_id') ne $gene_id) { #gene_id different, we replace it.
+											warn("Level3 ".$feature_level3->_tag_value('ID').": We replace the gene_id ".$feature_level3->_tag_value('gene_id')." by ".$gene_id.". We save original gene_id into $previous_tag_l1 attribute.\n");
+																create_or_replace_tag($feature_level3, $previous_tag_l1, $feature_level3->_tag_value('gene_id'));
+																create_or_replace_tag($feature_level3, 'gene_id', $gene_id);
+										}
+										#Check add transcript_id
+										if(! $feature_level3->has_tag('transcript_id')){
+											$feature_level3->add_tag_value('transcript_id', $transcript_id);
+										}
+										elsif($feature_level3->_tag_value('transcript_id') ne $transcript_id){ #transcript_id different, we replace it.
+											warn("Level3 ".$feature_level3->_tag_value('ID').": We replace the transcript_id ".$feature_level3->_tag_value('transcript_id')." by ".$transcript_id.". We save original transcript_id into $previous_tag_l2 attribute.\n");
+											create_or_replace_tag($feature_level3, $previous_tag_l2, $feature_level3->_tag_value('transcript_id'));
 											create_or_replace_tag($feature_level3, 'transcript_id', $transcript_id);
-	                  }
-	                }
-	              }
-	            }
-
-	            ## add level2 missing information gene_id
-	            if(! $feature_level2->has_tag('gene_id')) {
-	               $feature_level2->add_tag_value('gene_id', $gene_id);
-	            }
-	            elsif($feature_level2->_tag_value('gene_id') ne $gene_id) { #gene_id different, we replace it.
-	              warn("Level2 ".$feature_level2->_tag_value('ID').": We replace the gene_id ".$feature_level2->_tag_value('gene_id')." by ".$gene_id.". We save original gene_id into $previous_tag_l1 attribute.\n");
+										}
+									}
+								}
+							}
+
+							## add level2 missing information gene_id
+							if(! $feature_level2->has_tag('gene_id')) {
+								$feature_level2->add_tag_value('gene_id', $gene_id);
+							}
+							elsif($feature_level2->_tag_value('gene_id') ne $gene_id) { #gene_id different, we replace it.
+								warn("Level2 ".$feature_level2->_tag_value('ID').": We replace the gene_id ".$feature_level2->_tag_value('gene_id')." by ".$gene_id.". We save original gene_id into $previous_tag_l1 attribute.\n");
 								create_or_replace_tag($feature_level2, $previous_tag_l1, $feature_level2->_tag_value('gene_id'));
 								create_or_replace_tag($feature_level2, 'gene_id', $gene_id);
-	            }
-	            # add level2 missing information transcript_id
-	            if(! $feature_level2->has_tag('transcript_id')){
-	              $feature_level2->add_tag_value('transcript_id', $transcript_id);
-	            }
-	            elsif($feature_level2->_tag_value('transcript_id') ne $transcript_id){ #gene_id transcript_id, we replace it.
-	              warn("Level2 ".$feature_level2->_tag_value('ID').": We replace the transcript_id ".$feature_level2->_tag_value('transcript_id')." by ".$transcript_id.". We save original transcript_id into $previous_tag_l2 attribute.\n");
+							}
+							# add level2 missing information transcript_id
+							if(! $feature_level2->has_tag('transcript_id')){
+								$feature_level2->add_tag_value('transcript_id', $transcript_id);
+							}
+							elsif($feature_level2->_tag_value('transcript_id') ne $transcript_id){ #gene_id transcript_id, we replace it.
+								warn("Level2 ".$feature_level2->_tag_value('ID').": We replace the transcript_id ".$feature_level2->_tag_value('transcript_id')." by ".$transcript_id.". We save original transcript_id into $previous_tag_l2 attribute.\n");
 								create_or_replace_tag($feature_level2, $previous_tag_l2, $feature_level2->_tag_value('transcript_id'));
-	              create_or_replace_tag($feature_level2, 'transcript_id', $transcript_id);
-	            }
-	          }
-	        }
-	      }
-
-	      ## add level1 missing information gene_id
-	      if(! $feature_level1->has_tag('gene_id')) {
-	        $gene_id = $feature_level1->_tag_value('ID') if (! $gene_id);
-	        $feature_level1->add_tag_value('gene_id', $gene_id);
-	      }
-	      elsif($feature_level1->_tag_value('gene_id') ne $gene_id) { #gene_id different, we replace it.
-	        warn("Level1 ".$feature_level1->_tag_value('ID').": We replace the gene_id ".$feature_level1->_tag_value('gene_id')." by ".$gene_id.". We save original gene_id into $previous_tag_l1 attribute.\n");
+								create_or_replace_tag($feature_level2, 'transcript_id', $transcript_id);
+							}
+						}
+					}
+				}
+
+				## add level1 missing information gene_id
+				if(! $feature_level1->has_tag('gene_id')) {
+					$gene_id = $feature_level1->_tag_value('ID') if (! $gene_id);
+					$feature_level1->add_tag_value('gene_id', $gene_id);
+				}
+				elsif($feature_level1->_tag_value('gene_id') ne $gene_id) { #gene_id different, we replace it.
+					warn("Level1 ".$feature_level1->_tag_value('ID').": We replace the gene_id ".$feature_level1->_tag_value('gene_id')." by ".$gene_id.". We save original gene_id into $previous_tag_l1 attribute.\n");
 					create_or_replace_tag($feature_level1, $previous_tag_l1, $feature_level1->_tag_value('gene_id'));
 					create_or_replace_tag($feature_level1,'gene_id', $gene_id);
-	      }
+				}
 
 				# Save used ID
 				$keep_track_gene_id{$gene_id}++;
 				$keep_track_transcript_id{$transcript_id}++ if ($transcript_id);
-	    }
-	  }
+			}
+		}
 	}
 
 	if (! $relax){
 		# convert correct
 		_convert_feature_type($hash_omniscient, $gtf_version, $verbose);
-
 	}
 
 	# print results
@@ -432,7 +429,7 @@ sub _remove_cds{
 	@{$hash_omniscient->{'level3'}{'cds'}{$id_l2}} = @new_cds_list;
 }
 
-# Make a uniq string id for comprison.
+# Make a uniq string id for comparison.
 # Needed because ID is not enough because CDS can share identifiers
 sub _uniq_comparison{
 	my ($feature)=@_;
@@ -462,6 +459,7 @@ sub _print_omniscient_filter{
 
 			my $feature_l1 = $hash_omniscient->{'level1'}{$primary_tag_l1}{$id_tag_key_level1};
 			my $primary_tag_l1_gtf = lc($feature_l1->primary_tag());
+			_deal_with_double_attributes($feature_l1);
 			$gffout->write_feature($feature_l1); # print feature
 
 			# ----- LEVEL 2 -----
@@ -470,6 +468,7 @@ sub _print_omniscient_filter{
 					foreach my $feature_level2 ( sort { ncmp ($a->start.$a->end.$a->_tag_value('ID'), $b->start.$b->end.$b->_tag_value('ID') ) } @{$hash_omniscient->{'level2'}{$primary_tag_l2}{$id_tag_key_level1}}) {
 
 						my $primary_tag_l2_gtf = lc($feature_level2->primary_tag());
+						_deal_with_double_attributes($feature_level2);
 						$gffout->write_feature($feature_level2); # print feature
 
 						# ----- LEVEL 3 -----
@@ -480,6 +479,7 @@ sub _print_omniscient_filter{
 						# FIRST EXON
 						if ( exists_keys( $hash_omniscient, ('level3', 'exon', $level2_ID) ) ){
 							foreach my $feature_level3 ( sort {$a->start <=> $b->start} @{$hash_omniscient->{'level3'}{'exon'}{$level2_ID}}) {
+								_deal_with_double_attributes($feature_level3);
 								$gffout->write_feature($feature_level3);
 								push @l3_done, 'exon';
 							}
@@ -488,6 +488,7 @@ sub _print_omniscient_filter{
 						# SECOND CDS
 						if ( exists_keys( $hash_omniscient, ('level3', 'cds', $level2_ID) ) ){
 							foreach my $feature_level3 ( sort {$a->start <=> $b->start} @{$hash_omniscient->{'level3'}{'cds'}{$level2_ID}}) {
+								_deal_with_double_attributes($feature_level3);
 								$gffout->write_feature($feature_level3);
 								push @l3_done, 'cds';
 							}
@@ -501,6 +502,7 @@ sub _print_omniscient_filter{
 									my $primary_tag_l3_gtf = lc($hash_omniscient->{'level3'}{$primary_tag_l3}{$level2_ID}->[0]->primary_tag() );
 
 									foreach my $feature_level3 ( sort {$a->start <=> $b->start} @{$hash_omniscient->{'level3'}{$primary_tag_l3}{$level2_ID}}) {
+										_deal_with_double_attributes($feature_level3);
 										$gffout->write_feature($feature_level3);
 									}
 								}
@@ -513,6 +515,34 @@ sub _print_omniscient_filter{
 	}
 }
 
+# @Purpose: Modify the gene_id and transcript_id attributes to avoid double values
+# @input: 1 =>  feature
+# @output none => none
+sub _deal_with_double_attributes{
+	my ($feature) = @_  ;
+
+	if ($feature->has_tag('gene_id')){
+		my @gene_id_att = $feature->get_tag_values('gene_id');
+		if (scalar(@gene_id_att) > 1){
+			warn("Gene_id have several values, we will keep only the first one.\n");
+			my $gene_id = shift @gene_id_att; # get first value
+			$feature->remove_tag('gene_id');
+			$feature->add_tag_value('gene_id', $gene_id);
+			$feature->add_tag_value('agat_other_gene_id', @gene_id_att);
+		}
+	}
+	if ($feature->has_tag('transcript_id')){
+		my @transcript_id_att = $feature->get_tag_values('transcript_id');
+		if (scalar(@transcript_id_att) > 1){
+			my $transcript_id = shift @transcript_id_att; # get first value
+			warn("Transcript_id have several values, we will keep only the first one.\n");
+			$feature->remove_tag('transcript_id'); 
+			$feature->add_tag_value('transcript_id', $transcript_id);
+			$feature->add_tag_value('agat_other_transcript_id', @transcript_id_att);
+		}
+	}
+}
+
 # @Purpose: Print the headers when first time we access the fh
 # @input: 2 =>  ref omniscient, gff fh
 # @output none => none
diff --git a/lib/AGAT/OmniscientTool.pm b/lib/AGAT/OmniscientTool.pm
index 52c22b89..28b01cd5 100644
--- a/lib/AGAT/OmniscientTool.pm
+++ b/lib/AGAT/OmniscientTool.pm
@@ -382,7 +382,7 @@ sub merge_omniscients {
 			else{
 				#print "INFO level1:  Parent $id_l1 already exist. We generate a new one to avoid collision !\n";
 				my $feature = $hash_omniscient2->{'level1'}{$tag_l1}{$id_l1};
-				$uID = replace_by_uniq_ID( $feature, $hash_whole_IDs,  $hash2_whole_IDs, $miscCount);
+				$uID = replace_by_uniq_ID( $feature, $hash_whole_IDs,  $hash2_whole_IDs, $miscCount, "merge_omniscients");
 				$hash_omniscient1->{'level1'}{$tag_l1}{lc($uID)} = $hash_omniscient2->{'level1'}{$tag_l1}{$id_l1}; # save feature level1
 				$new_parent=1;
 			}
@@ -407,7 +407,7 @@ sub merge_omniscients {
 						if ( exists_keys ( $hash_whole_IDs,($id_l2) ) ){
 
 							#print "INFO level2:  Parent $id_l2 already exist. We generate a new one to avoid collision !\n";
-							$uID_l2 = replace_by_uniq_ID($feature_l2, $hash_whole_IDs,  $hash2_whole_IDs, $miscCount);
+							$uID_l2 = replace_by_uniq_ID($feature_l2, $hash_whole_IDs,  $hash2_whole_IDs, $miscCount, "merge_omniscients");
 							$new_parent_l2=1;
 						}
 						else{$hash_whole_IDs->{$id_l2}++;}
@@ -430,7 +430,7 @@ sub merge_omniscients {
 
 									if ( exists_keys ( $hash_whole_IDs,($id_l3) ) ){
 									#	print "INFO level3:  Parent $id_l3 already exist. We generate a new one to avoid collision !\n";
-										$uID_l3 = replace_by_uniq_ID($feature_l3, $hash_whole_IDs,  $hash2_whole_IDs, $miscCount);
+										$uID_l3 = replace_by_uniq_ID($feature_l3, $hash_whole_IDs,  $hash2_whole_IDs, $miscCount, "merge_omniscients");
 									}
 									else{$hash_whole_IDs->{$id_l3}++;}
 								}
@@ -563,9 +563,17 @@ sub merge_overlap_loci{
 							# update atttribute except ID and Parent for L1:
 							my @list_tag_l2 = $omniscient->{'level1'}{$tag_l1}{$id2_l1}->get_all_tags();
 							foreach my $tag (@list_tag_l2){
-								if(lc($tag) ne "parent" and lc($tag) ne "id"){
+								if(lc($tag) ne "parent" and lc($tag) ne "id" and lc($tag) ne "gene_id"){
 									my @tag_values = $omniscient->{'level1'}{$tag_l1}{$id2_l1}->get_tag_values($tag);
 									create_or_append_tag($omniscient->{'level1'}{$tag_l1}{$id_l1}, $tag , \@tag_values);
+								} else {
+									my @tag_values = $omniscient->{'level1'}{$tag_l1}{$id2_l1}->get_tag_values($tag);
+									foreach my $tag_value (@tag_values){
+										# the suffix merge_omniscients is added by merge_omniscients when ID had same name. No need to keep the fake ID provided
+										if ( $tag_value !~ /^merge_omniscients/ ) {
+											create_or_append_tag($omniscient->{'level1'}{$tag_l1}{$id_l1}, "merged_".$tag , $tag_value);
+										}
+									}
 								}
 							}
 							# remove the level1 of the ovelaping one
@@ -606,7 +614,12 @@ sub merge_overlap_loci{
 											my @list_tag_l2 = $common->get_all_tags();
 											foreach my $tag (@list_tag_l2){
 												my @tag_values = $common->get_tag_values($tag);
-												create_or_append_tag($kept_l2, "merged_".$tag , \@tag_values);
+												foreach my $tag_value (@tag_values){
+													# the suffix merge_overlap_loci is added by merge_omniscients when ID had same name. No need to keep the fake ID provided
+													if ( $tag_value !~ /^merge_omniscients/ ) {
+														create_or_append_tag($kept_l2, "merged_".$tag , $tag_value);
+													}
+												}
 											}
 										}
 									}
@@ -1875,13 +1888,15 @@ sub get_all_IDs{
 }
 
 # @Purpose: Replace ID by Uniq ID and modify all parent attribute of child feature to stay in line with the modification
-# @input: 4 => feature objetc, hash of ids, hash of ids, hash of feature counted to give more rapidly a name
+# @input: 5 => feature objetc, hash of ids, hash of ids, hash of feature counted to give more rapidly a name, prefix to choose a specific prefix (may be usefull for downstream process to recognize who/why asked for a new ID)
 # @output: uniq ID
 sub replace_by_uniq_ID{
-	my ($feature, $hash_whole_IDs, $hash2_whole_IDs, $miscCount) = @_;
+	my ($feature, $hash_whole_IDs, $hash2_whole_IDs, $miscCount, $prefix) = @_;
 
 	my $id = $feature->_tag_value('ID');
-	my $prefix = "IDmodified";
+	if (! $prefix){
+		$prefix = "IDmodified";
+	}
 	my $key;
 
 	if($prefix){
diff --git a/share/agat_config.yaml b/share/agat_config.yaml
index 3b9b87af..299053c4 100644
--- a/share/agat_config.yaml
+++ b/share/agat_config.yaml
@@ -17,6 +17,11 @@ gff_output_version: 3
 # relax = all feature types will be accepted
 gtf_output_version: relax
 
+# deflate multi-values attribute
+# GTF: attribute_tag "att_value1" "att_value2" "att_value3" => attribute_tag "att_value1"; attribute_tag2 "att_value2"; attribute_tag3 "att_value3"
+# GFF: attribute_tag=att_value1,att_value2,att_value3 => attribute_tag=att_value1;attribute_tag2=att_value2;attribute_tag3=att_value3;
+deflate_attribute: false
+
 # Integer - verbosity 0,1,2,3,4. 0 is quiet
 verbose: 1
 
diff --git a/t/config.t b/t/config.t
index 79ecaf6f..5dfbc7d3 100644
--- a/t/config.t
+++ b/t/config.t
@@ -40,6 +40,7 @@ system("$script config -e \\
 								--gff_output_version 2  \\
 								--gtf_output_version 2  \\
 								--debug  \\
+								--deflate_attribute  \\
 								--no-check_all_level1_locations  \\
 								--no-check_identical_isoforms  \\
 								--no-check_utrs  \\
diff --git a/t/config/out/agat_config.yaml b/t/config/out/agat_config.yaml
index 48715279..1537fadb 100644
--- a/t/config/out/agat_config.yaml
+++ b/t/config/out/agat_config.yaml
@@ -12,6 +12,7 @@ check_utrs: false
 clean_attributes_from_template: true
 create_l3_for_l2_orphan: false
 debug: true
+deflate_attribute: true
 force_gff_input_version: 3
 gff_output_version: 2
 gtf_output_version: 2
diff --git a/t/gff_other.t b/t/gff_other.t
index ae38a000..cca172a0 100644
--- a/t/gff_other.t
+++ b/t/gff_other.t
@@ -2,7 +2,7 @@
 
 use strict;
 use warnings;
-use Test::More tests => 8;
+use Test::More tests => 9;
 
 =head1 DESCRIPTION
 
@@ -101,7 +101,7 @@ $correct_output = "$output_folder/issue448.gtf";
 system("$script_agat config --expose --output_format gtf 2>&1 1>/dev/null");
 system("$script --g $input_folder/issue448.gtf -o $pathtmp  2>&1 1>/dev/null");
 
-ok( system("diff $pathtmp $correct_output") == 0, "issue441 check");
+ok( system("diff $pathtmp $correct_output") == 0, "issue448 check");
 
 unlink $pathtmp;
 unlink $config;
@@ -109,5 +109,17 @@ unlink $config;
 $correct_output = "$output_folder/issue448.gff";
 system("$script --g $input_folder/issue448.gtf -o $pathtmp  2>&1 1>/dev/null");
 
-ok( system("diff $pathtmp $correct_output") == 0, "issue441 check");
-unlink $pathtmp;
\ No newline at end of file
+ok( system("diff $pathtmp $correct_output") == 0, "issue448 check");
+unlink $pathtmp;
+
+# --------- Issue 457 multi-values attributes (gene_name "26266" "MT-TL1";) can be deflated to be compliant with GTF and CellRanger
+
+$script = $script_prefix."bin/agat_convert_sp_gff2gtf.pl";
+$correct_output = "$output_folder/issue457.gtf";
+
+system("$script_agat config --expose --deflate_attribute 2>&1 1>/dev/null");
+system("$script --gff $input_folder/issue457.gff -o $pathtmp  2>&1 1>/dev/null");
+
+ok( system("diff $pathtmp $correct_output") == 0, "issue457 check");
+unlink $pathtmp;
+unlink $config;
\ No newline at end of file
diff --git a/t/gff_other/in/issue457.gff b/t/gff_other/in/issue457.gff
new file mode 100644
index 00000000..48ff345d
--- /dev/null
+++ b/t/gff_other/in/issue457.gff
@@ -0,0 +1,4 @@
+##gff-version 3
+chrM	AGAT	gene	3230	3304	.	+	.	ID=agat-gene-1;gene_id=26266;gene_name=26266,MT-TL1;gene_type=misc_RNA;hgnc_id=HGNC:7490;level=3;merged_ID=ENSG00000209082.1;merged_gene_id=ENSG00000209082.1,26266;tag=basic,Ensembl_canonical;transcript_name=26266,MT-TL1-201;transcript_support_level=NA;transcript_type=misc_RNA
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	ID=26266;Parent=agat-gene-1;gene_id=26266;gene_name=26266;gene_type=misc_RNA;level=3;merged_ID=ENST00000386347.1;merged_Parent=ENSG00000209082.1;merged_gene_id=ENSG00000209082.1,26266;merged_gene_name=MT-TL1,26266;merged_gene_type=misc_RNA;merged_hgnc_id=HGNC:7490;merged_level=3;merged_tag=basic,Ensembl_canonical;merged_transcript_id=ENST00000386347.1,26266;merged_transcript_name=MT-TL1-201,26266;merged_transcript_support_level=NA;merged_transcript_type=misc_RNA;transcript_id=26266;transcript_name=26266;transcript_type=misc_RNA
+chrM	ENSEMBL	exon	3230	3304	.	+	.	ID=agat-exon-1;Parent=26266;gene_id=26266;gene_name=26266;gene_type=misc_RNA;level=3;transcript_id=26266;transcript_name=26266;transcript_type=misc_RNA
diff --git a/t/gff_other/out/issue457.gtf b/t/gff_other/out/issue457.gtf
new file mode 100644
index 00000000..93ba5861
--- /dev/null
+++ b/t/gff_other/out/issue457.gtf
@@ -0,0 +1,5 @@
+##gtf-version X
+# GFF-like GTF i.e. not checked against any GTF specification. Conversion based on GFF input, standardised by AGAT.
+chrM	AGAT	gene	3230	3304	.	+	.	gene_id "26266"; ID "agat-gene-1"; gene_name "26266"; gene_name_1 "MT-TL1"; gene_type "misc_RNA"; hgnc_id "HGNC:7490"; level "3"; merged_ID "ENSG00000209082.1"; merged_gene_id "ENSG00000209082.1"; merged_gene_id_1 "26266"; tag "basic"; tag_1 "Ensembl_canonical"; transcript_name "26266"; transcript_name_1 "MT-TL1-201"; transcript_support_level "NA"; transcript_type "misc_RNA";
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; ID "26266"; Parent "agat-gene-1"; gene_name "26266"; gene_type "misc_RNA"; level "3"; merged_ID "ENST00000386347.1"; merged_Parent "ENSG00000209082.1"; merged_gene_id "ENSG00000209082.1"; merged_gene_id_1 "26266"; merged_gene_name "MT-TL1"; merged_gene_name_1 "26266"; merged_gene_type "misc_RNA"; merged_hgnc_id "HGNC:7490"; merged_level "3"; merged_tag "basic"; merged_tag_1 "Ensembl_canonical"; merged_transcript_id "ENST00000386347.1"; merged_transcript_id_1 "26266"; merged_transcript_name "MT-TL1-201"; merged_transcript_name_1 "26266"; merged_transcript_support_level "NA"; merged_transcript_type "misc_RNA"; transcript_name "26266"; transcript_type "misc_RNA";
+chrM	ENSEMBL	exon	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; ID "agat-exon-1"; Parent "26266"; gene_name "26266"; gene_type "misc_RNA"; level "3"; transcript_name "26266"; transcript_type "misc_RNA";
diff --git a/t/gff_syntax/out/15_correct_output.gff b/t/gff_syntax/out/15_correct_output.gff
index 2bf3a620..29e7635d 100644
--- a/t/gff_syntax/out/15_correct_output.gff
+++ b/t/gff_syntax/out/15_correct_output.gff
@@ -4,7 +4,7 @@ scaffold625	maker	match_part	337818	337971	.	+	.	ID=CLUHART00000008717:exon:1404
 scaffold625	maker	match_part	340733	340841	.	+	.	ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717;Target=CLUHART00000008717 155 263
 scaffold625	maker	match_part	341518	341628	.	+	.	ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717;Target=CLUHART00000008717 264 374
 scaffold625	maker	match_part	341964	343277	.	+	.	ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717;Target=CLUHART00000008717 375 1688
-scaffold789	maker	match	558184	564780	.	+	.	ID=CLUHART00000006146;Parent=CLUHARG00000003852
+scaffold789	maker	match	558184	564780	.	+	.	ID=CLUHART00000006146;Parent=CLUHARG00000003852;merged_ID=CLUHART00000006147;merged_Parent=CLUHARG00000003852
 scaffold789	maker	match_part	558184	560123	.	+	.	ID=agat-exon-4;Parent=CLUHART00000006146;Target=CLUHART00000006146 1 1940;merged_ID=CLUHART00000006146:exon:995;merged_Parent=CLUHART00000006147;merged_Target=CLUHART00000006147 1 1940
 scaffold789	maker	match_part	561401	561519	.	+	.	ID=agat-exon-5;Parent=CLUHART00000006146;Target=CLUHART00000006146 1941 2059;merged_ID=CLUHART00000006146:exon:996;merged_Parent=CLUHART00000006147;merged_Target=CLUHART00000006147 1941 2059
 scaffold789	maker	match_part	562057	562121	.	+	.	ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006146;Target=CLUHART00000006147 2060 2124
diff --git a/t/gff_syntax/out/25_correct_output.gff b/t/gff_syntax/out/25_correct_output.gff
index 170b576f..da45d281 100644
--- a/t/gff_syntax/out/25_correct_output.gff
+++ b/t/gff_syntax/out/25_correct_output.gff
@@ -21,7 +21,7 @@ scaffold1	StringTie	exon	12106	13353	1000.00	-	.	ID=agat-exon-13;Parent=MSTRG.6.
 scaffold1	AGAT	gene	21499	23178	.	.	.	ID=agat-gene-3;geneID=MSTRG.7
 scaffold1	StringTie	transcript	21499	23178	1000.00	.	.	ID=MSTRG.7.1;Parent=agat-gene-3;geneID=MSTRG.7
 scaffold1	StringTie	exon	21499	23178	1000.00	.	.	ID=agat-exon-14;Parent=MSTRG.7.1;cov=207.398804
-scaffold1	AGAT	gene	44218	47964	.	-	.	ID=agat-gene-4;geneID=MSTRG.11
+scaffold1	AGAT	gene	44218	47964	.	-	.	ID=agat-gene-4;geneID=MSTRG.11;merged_ID=agat-gene-5,agat-gene-6
 scaffold1	StringTie	transcript	44218	47964	1000.00	-	.	ID=MSTRG.11.1;Parent=agat-gene-4;geneID=MSTRG.11
 scaffold1	StringTie	exon	44218	45365	1000.00	-	.	ID=agat-exon-15;Parent=MSTRG.11.1;cov=3001.629883
 scaffold1	StringTie	exon	47660	47706	1000.00	-	.	ID=agat-exon-16;Parent=MSTRG.11.1;cov=4399.870117
diff --git a/t/scripts_output.t b/t/scripts_output.t
index 487bb26b..d5da47ec 100644
--- a/t/scripts_output.t
+++ b/t/scripts_output.t
@@ -622,6 +622,12 @@ system(" $script --gff $input_folder/agat_sp_merge_annotations/fileA.gff  --gff
 ok( system("diff $result $outtmp") == 0, "output $script");
 unlink $outtmp;
 
+$result = "$output_folder/agat_sp_merge_annotations_3.gff";
+system(" $script --gff $input_folder/agat_sp_merge_annotations/test457_A.gff  --gff $input_folder/agat_sp_merge_annotations/test457_B.gff -o $outtmp 2>&1 1>/dev/null");
+#run test
+ok( system("diff $result $outtmp") == 0, "output $script");
+unlink $outtmp;
+
 # ------------------- check agat_sp_move_attributes_within_records script-------------------
 
 $script = $script_prefix."bin/agat_sp_move_attributes_within_records.pl";
diff --git a/t/scripts_output/in/agat_sp_merge_annotations/test457_A.gff b/t/scripts_output/in/agat_sp_merge_annotations/test457_A.gff
new file mode 100644
index 00000000..faff9ce3
--- /dev/null
+++ b/t/scripts_output/in/agat_sp_merge_annotations/test457_A.gff
@@ -0,0 +1,4 @@
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; gene_type "misc_RNA"; gene_name "26266"; transcript_type "misc_RNA"; transcript_name "26266"; level 3;
+chrM	ENSEMBL	exon	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; gene_type "misc_RNA"; gene_name "26266"; transcript_type "misc_RNA"; transcript_name "26266"; level 3;
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	gene_id "ENSG00000209082.1"; transcript_id "ENST00000386347.1"; gene_type "misc_RNA"; gene_name "MT-TL1"; transcript_type "misc_RNA"; transcript_name "MT-TL1-201"; level 3; transcript_support_level "NA"; hgnc_id "HGNC:7490"; tag "basic"; tag "Ensembl_canonical";
+chrM	ENSEMBL	exon	3230	3304	.	+	.	gene_id "ENSG00000209082.1"; transcript_id "ENST00000386347.1"; gene_type "misc_RNA"; gene_name "MT-TL1"; transcript_type "misc_RNA"; transcript_name "MT-TL1-201"; exon_number 1; exon_id "ENSE00002006242.1"; level 3; transcript_support_level "NA"; hgnc_id "HGNC:7490"; tag "basic"; tag "Ensembl_canonical";
diff --git a/t/scripts_output/in/agat_sp_merge_annotations/test457_B.gff b/t/scripts_output/in/agat_sp_merge_annotations/test457_B.gff
new file mode 100644
index 00000000..b158b5e3
--- /dev/null
+++ b/t/scripts_output/in/agat_sp_merge_annotations/test457_B.gff
@@ -0,0 +1,2 @@
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; gene_type "misc_RNA"; gene_name "26266"; transcript_type "misc_RNA"; transcript_name "26266"; level 3;
+chrM	ENSEMBL	exon	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; gene_type "misc_RNA"; gene_name "26266"; transcript_type "misc_RNA"; transcript_name "26266"; level 3;
\ No newline at end of file
diff --git a/t/scripts_output/out/agat_sp_complement_annotations_1.gff b/t/scripts_output/out/agat_sp_complement_annotations_1.gff
index 486495da..4c549de0 100644
--- a/t/scripts_output/out/agat_sp_complement_annotations_1.gff
+++ b/t/scripts_output/out/agat_sp_complement_annotations_1.gff
@@ -4,17 +4,17 @@
 NC_003070.9	RefSeq	gene	3631	5899	.	+	.	ID=IDmodified-gene-1;locus_tag=AT1G01010
 NC_003070.9	AGAT	mRNA	3631	5899	.	+	.	ID=NC_003070.9:NAC001;Parent=IDmodified-gene-1;locus_tag=AT1G01010
 NC_003070.9	RefSeq	exon	3631	3913	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
-NC_003070.9	RefSeq	exon	3996	4276	.	+	.	ID=IDmodified-exon-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
-NC_003070.9	RefSeq	exon	4486	4605	.	+	.	ID=IDmodified-exon-2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
-NC_003070.9	RefSeq	exon	4706	5095	.	+	.	ID=IDmodified-exon-3;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
-NC_003070.9	RefSeq	exon	5174	5326	.	+	.	ID=IDmodified-exon-4;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
-NC_003070.9	RefSeq	exon	5439	5899	.	+	.	ID=IDmodified-exon-5;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	3996	4276	.	+	.	ID=merge_omniscients-exon-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	4486	4605	.	+	.	ID=merge_omniscients-exon-2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	4706	5095	.	+	.	ID=merge_omniscients-exon-3;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	5174	5326	.	+	.	ID=merge_omniscients-exon-4;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	5439	5899	.	+	.	ID=merge_omniscients-exon-5;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
 NC_003070.9	RefSeq	CDS	3760	3913	.	+	0	ID=agat-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
-NC_003070.9	RefSeq	CDS	3996	4276	.	+	2	ID=IDmodified-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
-NC_003070.9	RefSeq	CDS	4486	4605	.	+	0	ID=IDmodified-cds-2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
-NC_003070.9	RefSeq	CDS	4706	5095	.	+	0	ID=IDmodified-cds-3;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
-NC_003070.9	RefSeq	CDS	5174	5326	.	+	0	ID=IDmodified-cds-4;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
-NC_003070.9	RefSeq	CDS	5439	5630	.	+	0	ID=IDmodified-cds-5;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	3996	4276	.	+	2	ID=merge_omniscients-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	4486	4605	.	+	0	ID=merge_omniscients-cds-2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	4706	5095	.	+	0	ID=merge_omniscients-cds-3;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	5174	5326	.	+	0	ID=merge_omniscients-cds-4;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	5439	5630	.	+	0	ID=merge_omniscients-cds-5;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
 NC_003070.9	AGAT	five_prime_UTR	3631	3759	.	+	.	ID=agat-five_prime_utr-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
 NC_003070.9	RefSeq	start_codon	3760	3762	.	+	0	ID=agat-start_codon-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
 NC_003070.9	RefSeq	stop_codon	5628	5630	.	+	0	ID=agat-stop_codon-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
diff --git a/t/scripts_output/out/agat_sp_merge_annotations_1.gff b/t/scripts_output/out/agat_sp_merge_annotations_1.gff
index 5f68f1f3..bb16cd3f 100644
--- a/t/scripts_output/out/agat_sp_merge_annotations_1.gff
+++ b/t/scripts_output/out/agat_sp_merge_annotations_1.gff
@@ -1,6 +1,6 @@
 ##gff-version 3
 chr10	BestRefSeq	gene	123237824	123357992	.	-	.	ID=gene-FGFR2;ontology=G0222
-chr10	BestRefSeq	mRNA	123237824	123357992	.	-	.	ID=rna-NM_022970.3;Parent=gene-FGFR2;ontology=G0222;merged_ID=IDmodified-mrna-1;merged_Ontology=G0333;merged_Parent=IDmodified-gene-1
+chr10	BestRefSeq	mRNA	123237824	123357992	.	-	.	ID=rna-NM_022970.3;Parent=gene-FGFR2;ontology=G0222;merged_Ontology=G0333
 chr10	BestRefSeq	exon	123237824	123239535	.	-	.	ID=exon-NM_022970.3-18;Parent=rna-NM_022970.3
 chr10	BestRefSeq	exon	123243212	123243317	.	-	.	ID=exon-NM_022970.3-17;Parent=rna-NM_022970.3
 chr10	BestRefSeq	exon	123353223	123353481	.	-	.	ID=exon-NM_022970.3-2;Parent=rna-NM_022970.3
diff --git a/t/scripts_output/out/agat_sp_merge_annotations_2.gff b/t/scripts_output/out/agat_sp_merge_annotations_2.gff
index 1c3846b2..0441a6c6 100644
--- a/t/scripts_output/out/agat_sp_merge_annotations_2.gff
+++ b/t/scripts_output/out/agat_sp_merge_annotations_2.gff
@@ -1,3 +1,3 @@
 ##gff-version 3
-chr1	AUGUSTUS	gene	1000424	1039237	.	+	.	ID=A
+chr1	AUGUSTUS	gene	1000424	1039237	.	+	.	ID=A;merged_ID=B
 chr1	AUGUSTUS	mRNA	1000424	1039237	.	+	.	ID=A.t1;Parent=A;merged_ID=B.t1;merged_Parent=B
diff --git a/t/scripts_output/out/agat_sp_merge_annotations_3.gff b/t/scripts_output/out/agat_sp_merge_annotations_3.gff
new file mode 100644
index 00000000..48ff345d
--- /dev/null
+++ b/t/scripts_output/out/agat_sp_merge_annotations_3.gff
@@ -0,0 +1,4 @@
+##gff-version 3
+chrM	AGAT	gene	3230	3304	.	+	.	ID=agat-gene-1;gene_id=26266;gene_name=26266,MT-TL1;gene_type=misc_RNA;hgnc_id=HGNC:7490;level=3;merged_ID=ENSG00000209082.1;merged_gene_id=ENSG00000209082.1,26266;tag=basic,Ensembl_canonical;transcript_name=26266,MT-TL1-201;transcript_support_level=NA;transcript_type=misc_RNA
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	ID=26266;Parent=agat-gene-1;gene_id=26266;gene_name=26266;gene_type=misc_RNA;level=3;merged_ID=ENST00000386347.1;merged_Parent=ENSG00000209082.1;merged_gene_id=ENSG00000209082.1,26266;merged_gene_name=MT-TL1,26266;merged_gene_type=misc_RNA;merged_hgnc_id=HGNC:7490;merged_level=3;merged_tag=basic,Ensembl_canonical;merged_transcript_id=ENST00000386347.1,26266;merged_transcript_name=MT-TL1-201,26266;merged_transcript_support_level=NA;merged_transcript_type=misc_RNA;transcript_id=26266;transcript_name=26266;transcript_type=misc_RNA
+chrM	ENSEMBL	exon	3230	3304	.	+	.	ID=agat-exon-1;Parent=26266;gene_id=26266;gene_name=26266;gene_type=misc_RNA;level=3;transcript_id=26266;transcript_name=26266;transcript_type=misc_RNA