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Table 1 Genomic coverage of genotype panels of SNP chip only and combined approach

From: A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

MAF bin Estimated r 2 ≥ 0.8 Estimated r 2 ≥ 0.4
Exome chip SNP chip Combined Exome chip SNP chip Combined
ALL 0.367 0.435 0.560 0.492 0.749 0.818
≥5 % 0.600 0.794 0.901 0.756 0.953 0.983
1–5 % 0.374 0.403 0.588 0.510 0.799 0.881
0.5–1 % 0.192 0.146 0.290 0.290 0.585 0.686
<0.5 % 0.107 0.079 0.172 0.192 0.491 0.591