United States Department of Agriculture
Agricultural Research Service
United States Department of Agriculture
Agricultural Research Service
| Genomic Summary | |
| Number of uploads | 105 |
| Number of Animals | 4244 |
| Number of Distinct Animals | 4043 |
| Known SNP Chips | |
| SNP Chip Name | Number of uploads |
| Affymetrix Axiom Chicken Array | 1 |
| Custom Oyster Chip - John Buchanan The Center for Aquaculture Technologies | 1 |
| GeneSeek Genomic Profiler (GCP) indicus | 1 |
| GeneSeek Genomic Profiler (GGP) Equine | 14 |
| GeneSeek-Neogen Porcine SNP80 BeadChip | 6 |
| GGP Bovine 100K | 6 |
| GGP Bovine HD150K Beadchip | 11 |
| GGP Ovine 50K | 4 |
| GGP Ovine 50K (Embrapa) | 1 |
| GGP Ovine 50K V2 | 1 |
| GGP Porcine 50K BeadChip | 2 |
| IGGC Caprine SNP50 BeadChip v1 | 6 |
| Illumina Bovine SNP50v1 BeadChip | 1 |
| Illumina Bovine SNP50v2 BeadChip | 9 |
| Illumina BovineHD BeadChip | 24 |
| Illumina Infinium Ovine SNP50 v1 BeadChip | 10 |
| Illumina Ovine HD BeadChip | 6 |
| Illumina Porcine SNP60 v2 BeadChip | 1 |
| Animals by SNP Chip (click chip name to download data) | |
| SNP Chip Name | Number of Animals |
| Affymetrix Axiom Chicken Array | 277 |
| Custom Oyster Chip - John Buchanan The Center for Aquaculture Technologies | 192 |
| GeneSeek Genomic Profiler (GCP) indicus | 76 |
| GeneSeek Genomic Profiler (GGP) Equine | 285 |
| GeneSeek-Neogen Porcine SNP80 BeadChip | 547 |
| GGP Bovine 100K | 298 |
| GGP Bovine HD150K Beadchip | 68 |
| GGP Ovine 50K | 7 |
| GGP Ovine 50K (Embrapa) | 16 |
| GGP Ovine 50K V2 | 77 |
| GGP Porcine 50K BeadChip | 48 |
| IGGC Caprine SNP50 BeadChip v1 | 110 |
| Illumina Bovine SNP50v1 BeadChip | 828 |
| Illumina Bovine SNP50v2 BeadChip | 100 |
| Illumina BovineHD BeadChip | 981 |
| Illumina Infinium Ovine SNP50 v1 BeadChip | 157 |
| Illumina Ovine HD BeadChip | 167 |
| Illumina Porcine SNP60 v2 BeadChip | 10 |
| Whole Genome Information | ||
| Sequence Name | Taxonomy | Number of Animals |
| John E. Rouse-Colorado State University Beef Improvement Center, WY | Bovidae Bos taurus - beef Angus CSU-BIC | 24 |
| Upload Details: Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format. The National Animal Germplasm Program has germplasm for this animal, with the repository number 45109. There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is attached. In the diagram, the two reads would correspond to read 1 and read 3. | https://scinet.usda.gov/ | |