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

	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
With Significant Blast hits	92		92.9%
SNP positions can be located by similarity comparisons with zebrafish genome	50		54.3%
Number of Loci with SNP predicted to be positioned at exon-intron border	32		64%
Total number of loci potentially with SNP positioned at exon-intron border	37		67.3%