Iam hiQ—a novel pair of accuracy indices for imputed genotypes

BMC Bioinformatics

Table 3 Q and Iam_chance by MAF

MAF	Q_chance	Q_HWE	Iam_chance based on Q_HWE
50%	0.667	0.625	0.0625
40%	0.667	0.614	0.0784
30%	0.667	0.575	0.1369
20%	0.667	0.486	0.2704
10%	0.667	0.311	0.5329
5%	0.667	0.176	0.7353
1%	0.667	0.039	0.9415
0.1%	0.667	0.0040	0.9940
0.01%	0.667	0.0004	0.9994
0.001%	0.667	0.00004	0.9999
0.0001%	0.667	0.000004	1.0000

MAF: minor allele frequency (\(f_{A}\)), Q_chance refers to a dosage of \(\left[ {\begin{array}{*{20}c} {1/3} & {1/3} & {1/3} \\ \end{array} } \right]\); Q_HWE refers to a dosage of \(\left[ {\begin{array}{*{20}c} {f_{A}^{2} } & {2f_{A}^{2} \left( {1 - f_{A} } \right)^{2} } & {1 - f_{A}^{2} } \\ \end{array} } \right]\)

ISSN: 1471-2105