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Table 1 Characteristics of in-silico SNPs subjected to verification by high-throughput genotyping

From: Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications

Gene groups

Total

Good SNP loci

Polymorphic SNP loci

no. (%)

MAF = 0 (n)

0 < MAF < 0.05 (n)

MAF ≥ 0.05 (n)*

SNP marker in total (%)

HCGs

162

118 (72.8%)

19

3

96

61.1%

DEGs

118

87 (73.7%)

20

3

64 (6)

56.8%

RGAs

152

96 (63.2%)

35

6

55 (6)

40.1%

Total

432

301 (69.7%)

74

12

215 (12)

52.50%

  1. Note (*): 12 SNP loci (six in RGAs and six in DEGs) showed 100% heterozygocity with MAF values at 0.5.