use strict;
use warnings;
use Data::Dumper;

my %clone_hash;

while (<DATA>) {
    my ($key, $value) = split;
    my $grade = ($value =~ /^pass[1-3]$/) ? 'good' : 'bad';
    $clone_hash{$key}{$grade}++;
}
print Dumper(\%clone_hash);

__DATA__
Eif2b2	fail
Eif2b2	pass5
Eif2b2	fail
Eif2b2	pass2
Eif2b2	fail
Eif2b2	pass4
Eif2b2	fail
49334	fail
49334	fail
49334	pass1
49334	fail
49334	pass4
Oxct1	pass4
Oxct1	fail
Oxct1	pass4
Oxct1	fail