Table 1 Description of different SNP chips and SNP subset panels
From: Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle
Label used for SNP panel in this study | SNP chip | Number of SNPs on chip | Filtered SNPs used in this study | Remarks |
|---|---|---|---|---|
15K | 15K (ParAllele/Affymatrix) | 15,036 | 205 SNPs from BTA20 | Â |
25K | 25K (Affymatrix) | 25,068 | 328 SNPs from BTA20 | Â |
50K | Illumina BovineSNP50 BeadChip | 54,001 | 42,136 | Â |
3K | Illumina BovineSNP50 BeadChip | 3,000 | 3,000 | Evenly spaced Subset of 50K |
5K | Illumina BovineSNP50 BeadChip | 5,000 | 5,000 | Evenly spaced Subset of 50K |
10K | Illumina BovineSNP50 BeadChip | 10,000 | 10,000 | Evenly spaced Subset of 50K |
20K | Illumina BovineSNP50 BeadChip | 20,000 | 20,000 | Evenly spaced Subset of 50K |
35K | Illumina BovineSNP50 BeadChip | 35,000 | 35,000 | Evenly spaced Subset of 50K |
BovineLD 7K | Illumina BovineLD BeadChip | 6,909 | 6,662 | Â |
Bovine3K | Illumina Bovine3K BeadChip | 2,900 | 2,500 | Â |
800K | Illumina 800K BovineHD beadChip | 786,799 | 610,879 | Â |
800K-imputed | Illumina 800K BovineHD beadChip | 786,799 | 610,879 | Imputed best guess genotypes |
800K-dosage | Illumina 800K BovineHD beadChip | 786,799 | 610,879 | Imputed dosage for B-allele |
49K | Illumina BovineSNP50 BeadChip | 54,001 | 49,394 | Common SNP between 800K and 50K chip |