Unlike concordance, the IQS results revealed that IMPUTE2 had the highest imputation accuracy when taking MAF into account for the 1000 Genomes (February 2012 release) reference panels (Figure 2). The IQS results for the three reference panels were nearly equivalent when using IMPUTE2. As shown in Figure S4, IMPUTE2 similarly outperformed the other programs when using reference panels from the older release of 1000 Genomes. The IQS metric is particularly useful for evaluating performance of low frequency SNPs, thus suggesting that the better performance by IMPUTE2 was driven by its markedly better imputation of low frequency SNPs.
