UNTESTED, but perhaps something like this:

use List::Util 'sum';

my @su_files = glob "SU*";
my @mu_files = glob "MU*";

@ARGV = ( @su_files, @mu_files );
my %data;
while ( <> ) {
    my ( $key, $number ) = split /\t/;
    push @{ $data{ $key }{ lc substr $ARGV, 0, 2 } }, $number;
    }

print join( "\t", 'Header', @su_files, 'average', @mu_files, 'average'
+ ), "\n";

for my $key ( sort keys %data ) {
    my ( $su, $mu ) = @{ $data{ $key } }{ qw/ su mu / };
    print join( "\t", $key, @$su, sum( @$su ) / @$su, @$mu, sum( @$mu 
+) / @$mu ), "\n";
    }
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