Table 5 Effect of low sequence quality (as defined by the presence of hot spots of SNP occurrence) and the presence of predicted intron on success rate of SNP genotyping
From: Quality assessment parameters for EST-derived SNPs from catfish
| Â | Tested | Succeeded | Percentage |
|---|---|---|---|
Number of loci with SNP located in regions containing low quality sequences | 14 | 7 | 50% |
Number of loci with known introns | 5 | 5 | 100% |
Number of failed loci without gene information | 99 | Â | Â |
With Significant Blast hits | 92 | Â | 92.9% |
SNP positions can be located by similarity comparisons with zebrafish genome | 50 | Â | 54.3% |
Number of Loci with SNP predicted to be positioned at exon-intron border | 32 | Â | 64% |
Total number of loci potentially with SNP positioned at exon-intron border | 37 | Â | 67.3% |