The relationship between IQS and imputation accuracy with respect to minor allele frequency is seen in Figure 1. Although imputation accuracy increases with decreased minor allele frequency, IQS drops dramatically with decreased minor allele frequency. Because it is known that low minor allele frequency decreases the quality of imputation, many studies drop SNPs with minor allele frequency less than 1%. According to this plot, this practice would still retain SNPs with an average IQS score of 88%, and would eliminate some well-imputed SNPs.
