In that scenario, our algorithm can condition on the strains that are already sequenced or strains imputed with high imputation accuracy, allowing researchers to identify the subset of low-confidence strains that can best be used to impute the full data set.
The imputed SNPs had a high imputation quality score.
The majority of the imputed SNPs had a high imputation quality score (MACH-R> 0.6).
All of the imputed SNPs had a high imputation quality score.
In a recent GWAS of coronary heart disease and its risk factors in a large African American sample [ 52], a high imputation concordance (95.6%) was obtained when SNPs were imputed using a combined reference panel of haplotypes from the HapMap phase II CEU and YRI panels.
We verified that the imputed markers included in genomic risk scores had high imputation accuracy (r > 0.8) in the training data.
These results demonstrated high imputation quality, even though nearly 10,000 SNPs within this 6-Mb region were imputed from the Affy 5.0 chip.
These results indicated that all the retained SNPs had a high imputation quality and were used for further analyses.
So, we decided to set the Info threshold at 0.60 as the threshold of high imputation quality.
high imputation AR cannot guarantee a power improvement in regions with low LD level; 4).
