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

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

Source of SNPs Number of successfully manufactured SNPs Segregating SNPs Failed SNPs
Number of segregating SNPs Genotyping success rate/true positive ratea Number of monomorphic SNPs Number of paralogous SNPsc Number of other non-segregating SNPsd Total number
Control SNPs recycled from previous genotyping arrays 89 76 85.4% 6 4 3 13 (14.6%)
Newly predicted SNPsb 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%)
  1. aGenotyping success rate for control SNPs, and true positive rate for newly discovered SNPs from exome capture and sequencing
  2. 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
  3. cParalogous SNPs, those with high excess of heterozygotes with Fe ≥ 0.80
  4. dOther non-segregating SNPs, those showing no clear clustering in two or three expected genotypic classes, or showing weak signal intensity