Table 2.
Descriptive statistics of the haplotype blocks with different linkage disequilibrium (LD) thresholds used in each scenario, before and after quality control (QC), in American Angus cattle.
| Descriptive | LD_0.15 | LD_0.50 | LD_0.80 |
|---|---|---|---|
| Number of non-clustered SNPs | 20,849 | 30,501 | 36,811 |
| Number of clustered SNPs | 21,784 | 12,132 | 5822 |
| Number of blocks | 9634 | 5617 | 2721 |
| Minimum number of SNP in blocks | 2 | 2 | 2 |
| Maximum number of SNP in blocks | 9 | 7 | 7 |
| Average (SD 1) block size (Mb) | 0.035 (0.020) | 0.032 (0.014) | 0.030 (0.013) |
| Minimum block size (bp) | 65 | 65 | 84 |
| Maximum block size (Mb) | 0.201 | 0.161 | 0.160 |
| Number of pseudo-SNPs 2 before QC | 56,734 | 27,324 | 12,877 |
| Number of pseudo-SNPs after QC | 44,559 | 23,918 | 11,389 |
| Number of non-clustered and pseudo-SNPs before QC | 77,583 | 57,825 | 49,688 |
| Number of non-clustered and pseudo-SNPs after QC | 65,435 | 54,444 | 48,227 |
1 Standard deviation. 2 Pseudo-SNPs are the unique haplotype alleles from the combination of phased SNPs within haplotype blocks.