Table 6 Parameters tested for genotype calling and imputation from an HD array
From: Fast imputation using medium or low-coverage sequence data
Dataset | Sequenced population | Array genotypes | |||||
|---|---|---|---|---|---|---|---|
SNVs | Population size | Sequence read depth | Error rate (%) | HD information included | SNPs/SNVs | Population size | |
Bovine (simulated) | 1,000,000 | 250 | 1×, 2×, 4×, 8×, 16× | 0, 1, 4, 16 | No | 20,000 | 250 |
Yes | 20,000 | 250 | |||||
500 | 1×, 2×, 4×, 8×, 16× | 0, 1, 4, 16 | Yes | 20,000 | 250 | ||
1000 | 1×, 2×, 4×, 8×, 16× | 0, 1, 4, 16 | Yes | 20,000 | 250 | ||
10,000 | 1×, 2× | 1 | Yes | 20,000 | 250 | ||
1000 | 8× | 1 | Yes | 3333 | 250 | ||
1000 | 8× | 1 | Yes | 1× sequence | 250 | ||
2× sequence | 250 | ||||||
Human (chromosome 22) | 394,724 | 884 | 1×, 2×, 4×, 8×, 16× | 0, 1, 4, 16 | Yes | 39,440 | 218 |