# Convert this:
values %{$hash_geno_group{$sample_geno_group}{$cds}{"rc"}}

# to this:
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"};