Table 1. Summary of performance of SNP by source.
| SNP source1 | Number of SNP available for selection2 | Estimated conversion rate (%)3 | Number of SNP selected for the BovineSNP504 (% of assay) | Number of SNP producing calls (%)5 | Number confirmed SNP (%)6 | Average MAF7 |
| Draft | 235,725 | 85 | 10,244 (17.6) | 9,361 (91.4) | 9,284 (99.1) | 0.24 |
| Interbreed | 73,127 | 84 | 6,035 (10.3) | 5,493 (91.0) | 5,244 (95.5) | 0.24 |
| BAC | 36,387 | 82 | 1,526 (2.6) | 1,409 (92.3) | 1,239 (87.9) | 0.24 |
| RRL | 65,180 | 92 | 25,833 (44.3) | 23,840 (92.3) | 21,914 (91.9) | 0.25 |
| HapMap | 29,853 | 1008 | 13,236 (22.7) | 12,613 (95.3) | 12,503 (99.1) | 0.26 |
| Parentage | 121 | 1008 | 121 (0.2) | 116 (95.9) | 116 (100) | 0.31 |
| Various | 4399 | 1008 | 1341 (2.3) | 1,169 (87.2) | 1,083 (92.6) | 0.26 |
| Total | 444,792 | NA9 | 58,336 | 54,001 (92.6) | 51,383 (95.1) | 0.26 |
1
Sources of SNP are defined in Materials and Methods.
2
The number of SNP input to the spacing/selection algorithm.
3
Percent of markers detected as polymorphic in validation studies which tested from 48 to 25,125 SNP.
4
BovineSNP50 is the name of the developed high-density genotyping assay.
5
Number of markers that produced genotype calls (>90% call rate) among the 556 tested animals.
6
Number of SNP for which at least one animal was heterozygous among the 556 tested animals and percent of the total number of markers producing genotype calls.
7
Average minor allele frequency among the 556 animals in the validation panel.
8
SNP selected from these sources had previously been shown to be informative in some populations.
9
NA = not applicable.