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'XM_010928396.1     ' => {
                                   'ambigu' => 156,
...
                                   'rc' => 195,
                                   'BC11_II_.RG' => 120
                                 },

# Convert this:
values %{$hash_geno_group{$sample_geno_group}{$cds}{"rc"}}
...
my $sample_geno_group_ref = $hash_geno_group{$sample_geno_group};
my $sample_cds = $sample_geno_group_ref->{$cds};
my $sample_rc = $sample_cds->{"rc"};