Table 5.
Relationship between minor allele frequency and the accuracy of imputation for reduced complexity semi-dependent datasets
| Minor allele frequency (MAF) |
||||||
|---|---|---|---|---|---|---|
| 0–0.1 | 0.1–0.2 | 0.2–0.3 | 0.3–0.4 | 0.4–0.5 | >0.1a | |
| No. sitesb | 1,029,330 | 156,251 | 97,013 | 73,001 | 66,296 | 392,561 |
| NAMgbs accuracy | 0.8707 | 0.9226 | 0.9168 | 0.9078 | 0.9126 | 0.9134 |
| NAMskim accuracy | 0.8015 | 0.8560 | 0.8782 | 0.8789 | 0.8900 | 0.8760 |
| Matchedc NAMgbs Acc. | 0.8763 | 0.9172 | 0.9102 | 0.8994 | 0.8992 | 0.9084 |
a
Summary of all groups where MAF > 0.1.
b
The sites within each MAF frequency bin were determined by frequency in the PHG database.
c
Data from NAMgbs for the same 24 lines sequenced for NAMskim.