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We observed that the proportion of missing genotypes varied considerably from SNP to SNP, but that missingness across individuals was consistent with a random allocation.
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Genotype imputation is an established method for inferring missing genotypes, although imputation accuracy can vary between populations and genomic regions (61).
aNumbers may vary because of missing genotypes.
The performance of the genotyping assay for each method was assessed using three criteria: missing genotypes (assay fail rates), incomplete genotypes (loci departing from HWE) and inaccurate genotypes (inconsistent genotypes across replicate samples).
This has resulted in high rates of missing genotypes (assay fail rates of 21%), incomplete genotypes (64% of loci departing from HWE) and inaccurate genotypes (1% of genotypes inconsistent across replicates).
SNPs with ≥2 missing genotypes were excluded.
Based on estimated parameters, missing genotypes are inferred.
The overall rate of missing genotypes was 9%.
Samples were screened for the proportion of missing genotypes, and animals with greater than 10% missing genotypes were removed.
Loci with >10% missing genotypes were discarded.
Genotype imputation refers to in silico reconstruction of missing genotypes.
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