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Minimac Diagnostics

9 bytes added, 11:35, 8 June 2017
Estimated Imputation Accuracy
The next column in the ''.info'' file lists the estimated frequency of allele 1 - this corresponds to the average number of imputed copies of allele 1 for each individual, divided by two.
=== Estimated Imputation Accuracy (ImpRsq) ===
Frequency information is followed by an estimate of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically <math>2p</math> where <math>p</math> is the frequency of the allele being imputed.

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