Table 1.
Number of unique, total, successfully called (high-quality genotype calls), and in the population segregating variants (SNPs and indels) on the DSN200k SNP chip per category of selection
| Categories of selection | # Unique variantsa | #Total variantsb | #Successfully called unique variants in DSN (n = 300) | #Successfully called unique variants across breeds (n = 462) | #Segregating unique variants (MAF > 0.01) in DSN |
|---|---|---|---|---|---|
| 1) Illumina BovineSNP50 DSN informative | 34,039 | 34,039 | 32,996 (96.94%) | 33,650 (98.96%) | 32,973 (96.87%) |
| 2) Associated with traits of interest (GWAS) | 1936 | 2071 | 1790 (92.46%) | 1869 (96.54%) | 1772 (91.53%) |
| 3) High, moderate, or low impact | 49,177 | 50,611 | 44,685 (90.87%) | 46,419 (94.39%) | 43,032 (87.50%) |
| 4) DSN unique | 37,388 | 38,198 | 32,579 (87.14%) | 33,348 (89.19%) | 25,903 (69.28%) |
| 5) High difference in alternative allele frequency between DSN and Holstein | 49 | 55 | 44 (89.80%) | 46 (93.88%) | 44 (89.80%) |
| 6) Y chromosome | 321 | 321 | 276 (85.98%) | 279 (86.92%) | 3 (0.93%) |
| 7) Mitochondria | 278 | 278 | 258 (92.81%) | 258 (92.81%) | 22 (7.91%) |
| 8) Parentage panels | 64 | 554 | 63 (98.44%) | 63 (98.44%) | 62 (96.88%) |
| 9) Haplotype blocks | 58,886 | 103,801 | 53,863 (91.47%) | 55,855 (94.85%) | 52,864 (89.77%) |
| 10) Filing gaps > 250 kb | 16 | 16 | 9 (56.25%) | 11 (68.75%) | 9 (56.25%) |
| Total | 182,154 | 166,563 (91.44%) | 171,798 (94.31%) | 156,684 (86.02%) |
aUnique variant refers to variants selected per category of selection without overlaps, given the selection order
bThe total number includes all variants per category, independently of selection order