Chargaff''s rule is not applicable for organellar genomes such as mitochondria and plastids because they are too small (20-30kbp).
In bacteriophage, the base pair rule cannot be applied. Their genomes contain more purines than pyrimidines.
The rule applies to only 5 types of double-stranded genomes like eukaryotic chromosomes, the bacterial chromosomes, double-stranded DNA viral genomes and the archaeal chromosomes.
It does not apply to single-stranded DNA (viral) genomes or any type of RNA genome.