Table 1.
Number (n) of SNP used to estimate linkage disequilibrium (LD), integrated extended haplotype homozygosity, and for regression of allele frequency on cumulative selection differential in Line 1 Hereford (L1) and the general Hereford population (AHA).
| Analysis | Linkage disequilibrium1 | Integrated extended haplotype homozygosity2 | Regression3 |
|---|---|---|---|
| Number of SNP | Number of SNP | Number of SNP | |
| L1 | 35,385 | 50,367 | 25,901 |
| AHA | 35,385 | 50,367 | NA |
1 All SNP that passed quality control and had minor allele frequency (MAF) > 2% in L1 were used in estimation of LD.
2 All SNP that passed quality control were used to estimate integrated extended haplotype homozygosity.
3 All SNP that passed quality control, had MAF > 2%, and were not in LD with another SNP on the same chromosome were used in regression analysis.