Table 1.
Summary of success rates when testing two strategies for SNP discovery in a set of target genes
| SNP discovery strategies tested: | 3'UTR-primed SNP discovery approach | in silico SNP mining approach |
|---|---|---|
| Number of genes (cCDS-FLIcs) tested | 208 | 168 |
| candidate SNPs success rate1 | - | 0.82 (131/168) |
| Initial PCR and sequencing success rate2 | 0.79 (165/208) | 0.47 (61/131) |
| SNP discovery rate3 | 0.45 (74/165) | 0.41 (25/61) |
| SNP discovery success rate4 | 0.36 (74/208) | 0.15 (25/168) |
1Number of target genes with at least one putative SNP/total number of target genes selected for testing the in silico SNP mining method. 2Number of primer pairs producing PCR fragments suitable for sequence analysis/total number of primer pairs tested. 3SNP discovery rate: one or more SNP discovered/PCR fragments analysed in the small population materials. 4SNP discovery success rate: genes with at least one SNP discovered/total number of genes tested.