Simpute: An Efficient Solution for Dense Genotypic Data

Table 3

A 3 × 3 contingency table for the genotypes at two consecutive loci. A and a are the two alleles in locus 1 while B and b are the two alleles in locus 2.

	0 (bb)	1 (bB)	2 (BB)	Total
0 (aa)	𝑁0,0	𝑁0,1	𝑁0,2	𝑁0,⋅
1 (aA)	𝑁1,0	𝑁1,1	𝑁1,2	𝑁1,⋅
2 (AA)	𝑁2,0	𝑁2,1	𝑁2,2	𝑁2,⋅
Total	𝑁⋅,0	𝑁⋅,1	𝑁⋅,2	𝑁𝑃,𝑄