use v5.14;

open(TEST,'<',"test.txt") or die $!;
my @test_data = <TEST>;
close(TEST);

open(REFERENCE,'<',"reference.txt") or die $!;
my @reference_data = <REFERENCE>;
close(REFERENCE);

my @results;

for my $line(@test_data){
   my $lesser_val = 9999999999999999;

   my($chr,$val) = split(/    /,$line);
   
   for my $ref_line(@reference_data){
      my($ref_chr,$ref_val) = split(/    /,$ref_line);

      if($ref_chr eq $chr){
         $lesser_val = ($ref_val-$val) if ($ref_val-$val < $lesser_val);
      }      
   }
   push(@results,"$chr    $lesser_val");  
}

say foreach @results;