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$VAR1 = {
          'A2M' => [
                     'C972Y',
...
                        'A219V'
                      ]
        };

gene total x
A2M 2 0
A4GALT 4 1

my %hash;
while(<INFILE>)
...
    my ($key, @val) = split /\t/, $line, 2;
    push @{ $hash{$key} }, @val;
}

my $totalcount = 0;
my $xcount = 0;
...
    
    print $k . "\t" . $totalcount . "\t" . $xcount . "\n";