Figure 2.

Variant representation in three common variant file specifications. A: The two variants are listed from sample NA12878 from the 1000Genomes database. Variant 1 is a deletion of A, and variant 2 is a substitution of A to G. The dbSNP identifiers, chromosome number, nucleotide change, and the predicted effect are shown. The Human Genome Variation Society nomenclature for the change is shown relative to the genomic DNA, the mRNA, and protein RefSeq sequences. B: Contrast the differences among the variant file specifications for each of the two variants. The genome variant call format (gVCF) includes the invariant regions, not typically reported by the VCF. The genome variation format (GVF) includes additional annotation of the effect of the variant on the reference annotated features. SNV, single-nucleotide variants.