diff --git a/modules/Bio/EnsEMBL/VEP/Stats.pm b/modules/Bio/EnsEMBL/VEP/Stats.pm
index 3287b7ee0..c371e7dfe 100644
--- a/modules/Bio/EnsEMBL/VEP/Stats.pm
+++ b/modules/Bio/EnsEMBL/VEP/Stats.pm
@@ -742,7 +742,13 @@ sub sort_keys {
   # sort data
   if(defined($sort)) {
     if($sort eq 'chr') {
-      @keys = sort {($a !~ /^\d+$/ || $b !~ /^\d+/ || $a =~ /^\d\w/ || $b =~ /^\d\w/ ) ? $a cmp $b : $a <=> $b} keys %{$data};
+      @keys = sort {                         
+        (my $aterm = $a) =~ s/chr//;
+        (my $bterm = $b) =~ s/chr//;
+        $aterm = ord($aterm) unless $aterm =~ /^\d+$/;
+        $bterm = ord($bterm) unless $bterm =~ /^\d+$/;
+        return $aterm <=> $bterm;
+      } keys %{$data};
     }
     elsif($sort eq 'value') {
       @keys = sort {$data->{$a} <=> $data->{$b}} keys %{$data};