Table 4. Distribution of classified SNPs across the discovery sets and success rates of these SNPs on the CottonSNP63K array.
| Data Set | SNPs on Array | Failed | Successful Assays (No.) | Success Rate (%) | |||
|---|---|---|---|---|---|---|---|
| No. | % | Monomorphic | Intergenomic | Polymorphic | |||
| Brigham Young University | 185 | 23 | 12.43 | 16 | 5 | 141 | 76.22 |
| CSIR-NBRI | 343 | 41 | 11.95 | 84 | 116 | 102 | 29.74 |
| USDA-Set1 | 104 | 10 | 9.62 | 81 | 4 | 9 | 8.65 |
| UC-Davis/TAMU GH RNA-Seq | 938 | 153 | 16.31 | 81 | 66 | 638 | 68.02 |
| USDA Set 2 | 2223 | 474 | 21.32 | 193 | 372 | 1184 | 53.26 |
| CSIRO | 17,230 | 2048 | 11.89 | 4325 | 772 | 10,085 | 58.53 |
| TAMU/UC-Davis Intra Genomic Set 1 | 23,418 | 3509 | 14.98 | 4639 | 3565 | 11,705 | 49.98 |
| UC-Davis/TAMU Intra Genomic Set 2 | 445 | 48 | 10.79 | 5 | 41 | 351 | 78.88 |
| DOW AgroSciences | 218 | 13 | 5.96 | 1 | 0 | 204 | 93.58 |
| UC-Davis Inter | 143 | 10 | 6.99 | 0 | 1 | 132 | 92.31 |
| CIRAD | 145 | 20 | 13.79 | 14 | 27 | 84 | 57.93 |
| TAMU/UC-Davis Inter RNA-Seq | 13,055 | 913 | 6.99 | 374 | 307 | 11,461 | 87.79 |
| TAMU/UC-Davis Inter Genomic | 4611 | 595 | 12.90 | 501 | 789 | 2726 | 59.12 |
| Total | 63,058 | 7857 | 12.46 | 10,314 | 6065 | 38,822 | 61.57 |