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Minimac Diagnostics

341 bytes added, 09:59, 21 October 2010
Basic Descriptors
== Basic Descriptors ==
=== Marker and Allele Labels ===
The first three columns in the ''.info'' file list marker name and alleles for each marker. Typically, the most common allele will be listed first, but this is not guaranteed.
=== Estimated Allele Frequency ===
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 ===
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.
:<math>\hat{r}^2 = {{Var(\mbox{Estimated Counts})}\over{\hat{p}(1-\hat{p})}}</math>
== Leave One Out Statistics ==
=== looRsq : Estimated R-squared in Leave-One-Out Analysis ===
=== empR : Correlation Between Imputed and True Genotypes ===
=== empRsq : Squared Correlation Between Imputed and True Genotypes ===

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