Table 2.

Representations of genetic and genomic data

Variant type	Description	How coded
SNPs	Single-nucleotide polymorphisms	ACGT or 0/1 (presence/absence for each allele copy relative to the alleles found in the map file)
Indels	Insertions/deletions	0/1 (presence/absence) or copy number (e.g., 0/1/2, etc. of the repeat polymorphism)
CNVs	Copy-number variants	Number of copies of the copy-number variants and map position boundaries of the variants
STRs	Short tandem repeats	Number of copies of the repeat (integer)
WGS/WES	Whole-genome/whole-exome sequences	ACGT. Can be full sequence or limited to just the variant positions relative to the reference sequence

ACGT: nucleotide base sequence such as adenine, cytosine, guanine, thymine.