Table 4.
Dataset ID | Description | Min. read depth | MinMAFa | Min. call rate | Number of variants | Variants shared with SNP50 | Imputation program | Estimated accuracy (%) |
---|---|---|---|---|---|---|---|---|
9 | GBS | 3 | 0.05 | 0.2 | 53,556 | 431 | FImpute | 71.1 |
10 | GBS + SNP50 | 3 | 0.05 | 0.2 | 98,398 | 431 | FImpute | 84.8 |
11 | GBS | 3 | 0.05 | 0.3 | 40,208 | 334 | FImpute | 74.2 |
12 | GBS + SNP50 | 3 | 0.05 | 0.3 | 88,573 | 334 | FImpute | 89.1 |
13 | GBS | 3 | 0.05 | 0.4 | 21,561 | 156 | FImpute | 77.5 |
14 | GBS + SNP50 | 3 | 0.05 | 0.4 | 70,250 | 156 | FImpute | 91.9 |
15 | GBS | 4 | 0.02 | 0.2 | 55,727 | 395 | FImpute | 73.3 |
16 | GBS + SNP50 | 4 | 0.02 | 0.2 | 100,297 | 395 | FImpute | 86.4 |
17 | GBS | 4 | 0.05 | 0.2 | 45,447 | 369 | Beagle | 70.9 |
GBS | 4 | 0.05 | 0.2 | 45,447 | 369 | FImpute | 71.2 | |
18 | GBS + SNP50 | 4 | 0.05 | 0.2 | 90.234 | 369 | Beagle | 78.5 |
GBS + SNP50 | 4 | 0.05 | 0.2 | 90.234 | 369 | FImpute | 86.1 | |
19 | GBS | 4 | 0.02 | 0.3 | 40,855 | 278 | FImpute | 75.9 |
20 | GBS + SNP50 | 4 | 0.02 | 0.3 | 89,196 | 278 | FImpute | 90.3 |
21 | GBS | 4 | 0.05 | 0.3 | 31,662 | 254 | Beagle | 74.0 |
GBS | 4 | 0.05 | 0.3 | 31,662 | 254 | FImpute | 74.3 | |
22 | GBS + SNP50 | 4 | 0.05 | 0.3 | 80,190 | 254 | Beagle | 83.8 |
GBS + SNP50 | 4 | 0.05 | 0.3 | 80,190 | 254 | FImpute | 89.3 | |
23 | GBS | 4 | 0.02 | 0.4 | 22,331 | 98 | FImpute | 83.3 |
24 | GBS + SNP50 | 4 | 0.02 | 0.4 | 70,983 | 98 | FImpute | 93.4 |
25 | GBS | 4 | 0.05 | 0.4 | 14,909 | 82 | Beagle | 81.2 |
GBS | 4 | 0.05 | 0.4 | 14,909 | 82 | FImpute | 80.8 | |
26 | GBS + SNP50 | 4 | 0.05 | 0.4 | 63,706 | 82 | Beagle | 89.8 |
GBS + SNP50 | 4 | 0.05 | 0.4 | 63,706 | 82 | FImpute | 93.4 | |
27 | GBS | 5 | 0.05 | 0.2 | 36,913 | 299 | FImpute | 70.0 |
28 | GBS + SNP50 | 5 | 0.05 | 0.2 | 81,454 | 299 | FImpute | 85.4 |
29 | GBS | 5 | 0.05 | 0.3 | 22,685 | 166 | FImpute | 74.8 |
30 | GBS + SNP50 | 5 | 0.05 | 0.3 | 71,360 | 166 | FImpute | 89.5 |
31 | GBS | 5 | 0.05 | 0.4 | 8818 | 42 | FImpute | 79.5 |
32 | GBS + SNP50 | 5 | 0.05 | 0.4 | 57,719 | 42 | FImpute | 92.2 |
aMinMAF: minimum minor allele frequency