Table 1 Number of single nucleotide polymorphisms for each data edit implemented on each density panel
Genotype edit | HD Panel | Reduced HD Panel | Hapmap SNP50 | Gautier SNP50 |
|---|---|---|---|---|
Initial data set | 777,962 (891) | 48,734 (891) | 54008 (533) | 58336 (633) |
Autosomes only | 735,293 (891) | 47,270 (891) | 51587 (533) | 55200 (633) |
SNP and animals with >90 % Call Rate | 727,559 (867) | 46,761 (867) | 50824 (530) | 44687 (633) |
Hardy Weinburg Equilibrium in each breed (p < 0.0001) | 723,502 (867) | 46,379 (867) | 50783 (530) | 44602 (633) |
Monomorphic SNPs removed | 665,058 (867) | 43,028 (867) | 48128 (530) | 44160 (633) |