Forget about it. Flip-Flop was okay, just replaced

while ( ($GeneID, $BMB) = each %hash) {
print "$GeneID => $BMB[0]\n";
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with

foreach my $key (keys %hash) {
    foreach my $val (@{$hash{$key}}) {
        print "$key --> $val\n";
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and now everything is fine. Thanks for the help