A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies)

Table 1 Genotyping success rate of the Picea abies Infinium SNP array and true positive rate according to sources of SNPs

Source of SNPs	Number of successfully manufactured SNPs	Segregating SNPs		Failed SNPs
Source of SNPs	Number of successfully manufactured SNPs	Number of segregating SNPs	Genotyping success rate/true positive rate^a	Number of monomorphic SNPs	Number of paralogous SNPs^c	Number of other non-segregating SNPs^d	Total number
Control SNPs recycled from previous genotyping arrays	89	76	85.4%	6	4	3	13 (14.6%)
Newly predicted SNPs^b from exome capture and sequencing	5571	4692	84.2%	304	504	71	879 (15.8%)
Total	5660	4768	84.2%	310	508	74	892 (15.8%)

^aGenotyping success rate for control SNPs, and true positive rate for newly discovered SNPs from exome capture and sequencing
^bSNPs identified among the 61,771 SNPs predicted by both PLATYPUS and GS REFERENCE MAPPER and satisfying the quality filters detailed in Materials and Methods
^cParalogous SNPs, those with high excess of heterozygotes with F_e ≥ 0.80
^dOther non-segregating SNPs, those showing no clear clustering in two or three expected genotypic classes, or showing weak signal intensity

ISSN: 1471-2164