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Table 8 Characteristics of 5847 successful SNPs based on data from an Illumina Infinium SNP array *

From: A SNP resource for Douglas-fir: de novotranscriptome assembly and SNP detection and validation

SNP characteristic Mean Median Range
GenTrain score 0.81 0.84 0.35-0.98
GC50 score (median GenCall score) 0.78 0.87 0.15-0.99
Call frequency 0.99 1.00 0.85-1.00
Minor allele frequency (MAF) 0.24 0.24 0.002-0.5
Heterozygosity (observed) 0.33 0.36 0.00-1.00
Heterozygosity (expected) 0.32 0.36 0.004-0.5
Number of SNPs with a significant HWE deviation = 263 (4.5%)§
  1. *Successful SNPs are those with a call frequency > 0.85 and MAF > 0 based on an analysis of 260 trees.
  2. Successful calls are those with a GenCall score ≥ 0.15 [19].
  3. § Tested using an exact test of HWE and a probability level of 0.9 × 10-5 (i.e., Bonferroni-corrected P-value of 0.05 based on 5847 SNPs).