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The added value (ie mean increase in imputation quality) was largest when comparing GoNL with 1000G in imputing the Dutch samples.
Thus, the increment in imputation quality was largest when the minor allele frequencies of the imputed variants were below 1%%.
An investigation of the source of differences in imputation accuracy revealed dependence on the MAF of the SNPs being imputed, and on the underlying LD structure.
Involving knowledge base in imputation could overcome this shortcoming.
Table 5 Estimates used in imputation of household income.
Geographic patterns in prediction uncertainties implicated biogeography and disturbance as major factors influencing regional variation in imputation uncertainty.
In most populations, each 1% increase in imputation error leads to an increase of ∼5%13%% in the sample size required for maintaining power.
The compounding of small error rates in components of the NPC class code leads to a 47% ± 10% rate of success over failure in imputation of the class a stand might later be assigned based on relevé data.
However, in imputation analysis, inserting zero or median in place of missing data did not affect the overall results.
The figures also show a slight increase in imputation performance as the size of the reference panel increased.
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However, our results suggest that even with 10% missing genotypes multiple-locus inference is served just as well by simpler "plug-in" imputation estimates (hard and dosage).
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