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There is a difference between the range of genomic sequences analysed and the types of variants that can be analysed.

1) Sequence coverage
3B-GENOME analyses all 3 billion genomic sequences, while 3B-EXOME only analyses the protein-coding regions of 20,000 genes.
2) Types of variants that can be analysed
While 3B-GENOME can analyse all types of variants, 3B-EXOME can only analyse SNVs, Indels and CNVs (contiguous variants in 3 or more exons). SV variants can only be analysed in 3B-GENOME.