Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

Table 4 Genotyping success rate. Genotyping success rate according to a priori Illumina functionality scores of SNPs for the GoldenGate assay for each of white spruce and black spruce.

Species	Class of functionality scores	Predicted functionality¹	Number of SNPs on SNP bead array	Number of valid SNPs detected²	Overall success rate (%)²	Number of monomorphic SNPs	Number of failed SNPs
White spruce
	0.1–0.4	low	18	8	44.4	2	8
	0.4–0.6	medium	71	27	38.0	6	38
	0.6–1.0	high	679	481	70.8	74	124
	Total	-	768	516	-	82	170
	Weighted average	-	-	-	67.2	-	-
Black spruce
	0.1–0.4	low	4	2	50.0	0	2
	0.4–0.6	medium	70	37	52.9	3	30
	0.6–1.0	high	694	553	79.7	34	107
	Total	-	768	592	-	37	139
	Weighted averaged	-	-	-	77.1	-	-

ISSN: 1471-2164