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Figure 4 shows a bubble plot of actual and incorrectly imputed genotypes for each of the six imputation methods.
Erbe et al. [ 20] studied imputation to the HD-chip and found more than 20% incorrectly imputed genotypes for each SNP in a subset of 1231 SNPs.
AlphaImpute with phasing, which used the haplotype library, resulted in more correctly imputed genotypes per individual but also in more incorrectly imputed genotypes per individual, which led to a lower animal-specific imputation accuracy than segregation analysis (Table 3).
The increase in incorrectly imputed SNPs per individual is due to the long-range haplotype imputation algorithm in AlphaImpute, which allows a certain mismatch (set to 1% in this study) between SNPs of the most likely haplotype from the haplotype library and (in a previous step imputed) genotypes of the imputed individual.
For each scenario and each category, the mean animal-specific imputation accuracy and its standard deviation, the percentage of correctly and incorrectly imputed SNP genotypes per individual and the percentage of genotypes not imputed per individual were calculated across the 10 replicates.
For incorrectly imputed genotypes it is possible to impute one or both alleles incorrectly.
Similar(33)
This assumption incorrectly imputes LC as the cause of death among many persons whose decision, without doubt, reflects their or their physician's recognition of manifest lethal comorbidities.
By imputing in individuals with few missing values but excluding individuals with more missing data, IPW/MI could inherit some of the efficiency advantage of MI while avoiding bias resulting from incorrectly imputing larger blocks of data.
Five percent or fewer of the missing high-density marker genotypes were imputed incorrectly.
We felt that the most serious threat to validity was data imputed incorrectly between the last observed value and death.
The thresholds for these selection criteria were chosen so that monomorphic SNPs and SNPs that are likely to be imputed incorrectly were removed.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com