Table 1 Overview of the different scenarios
From: The effect of rare alleles on estimated genomic relationships from whole genome sequence data
Scenario names | Type of data | Minor allele frequency threshold (%) | Number of segregating variants |
|---|---|---|---|
A ped | Pedigree | None | 0 |
G SNP5+ | BovineSNP50 BeadChip | ≥ 5 | 41 225 |
G SNP1+ | BovineSNP50 BeadChip | ≥ 1 | 44 548 |
G SNP1_5 | BovineSNP50 BeadChip | Between 1 and 5 | 3 323 |
G WGS5+ | Whole genome sequence | ≥ 5 | 11 953 905 |
G WGS1+ | Whole genome sequence | ≥ 1 | 15 871 933 |
G WGS1_5 | Whole genome sequence | Between 1 and 5 | 3 918 028 |