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The reason for a slightly higher genotype error rate than allele error rate for X-specific markers was that some genotypes were heterozygous in the real 54K data (due to typing error) and in the imputed data (due to imputation error).
Note, in this scenario, nij may not be an integer due to imputation probabilities being reported rather than imputed genotypes.
Although we assumed that all discrepancies between the imputed and sequenced-derived genotypes were due to imputation errors, it is clear that discrepancies could also be caused by sequencing errors.
Multiple imputation is also employed to assess the uncertainty due to imputation since results based on imputation alone, especially when linking imputed locations to other spatial data, may be questionable.
Therefore, the observed distortion was due to imputation error and the statistically skewed SNPs (Fig. 2B) are false positives.
Contrary to this, the larger number of nongeocodes in need of imputation due to the relative size of counties may impart some inaccuracy due to imputation to adjacent counties.
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Pszczola et al. [ 6] showed no significant improvement in accuracy of genomic prediction from adding imputed genotypes due to low imputation accuracy, although a slight improvement was seen with low heritabilities.
Imputation error or loss of information due to incomplete imputation could impact the accuracy of the estimated Mendelian sampling term only and not the parental average component or it might in turn influence only the accuracy of the dam's contribution to the estimated breeding value.
We find that it is more difficult to impute non-European samples, which is due to our imputation towards the GoNL reference panel.
The complementary approach of multiple imputation can then be applied to assess uncertainty due to the imputation process.
An additional 3 SNPs were removed due to poor imputation quality or ambiguous coding.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com