The remaining SNPs were referred to as untyped SNPs and their genotypes were subject to be imputed by imputation methods.
Considering the proportion of SNPs to be imputed (99.1%), the imputation accuracy was high even for the 7 K chip.
As imputation accuracy depends (amongst others) on the degree of relationship between sequenced individuals and individuals to be imputed, we also checked how imputing accuracy changes when different numbers of generations are between sequenced individuals and individuals to be imputed.
It is clear that to ensure effective imputation, the dataset to be imputed should contain related individuals.
IMPUTE2 uses linkage disequilibrium information to perform imputation, requires each individual to be imputed to have some SNP genotypes and does not use pedigree information.
Correlations of real and imputed genotypes remained constantly high even if individuals to be imputed were several generations away from the sequenced individuals.
In this case, imputation requires that the haplotypes of the individuals to be imputed are (at least partially) represented in the haplotype libraries.
It is pertinent to note at this point that imputation using chained equations does not require the variables to be imputed in a specific order.
As documented in the literature [ 4, 16], imputation accuracy increases with a decreasing proportion of SNPs to be imputed.
As Johnson himself said in prefacing his Dictionary: "Many seeming faults are to be imputed rather to the nature of the undertaking, than the negligence of the performer".
Each set of results requires a lot of work to collect the right information to be imputed and to develop software procedures.
