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

BMC Genomics

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

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%)^§

^*Successful SNPs are those with a call frequency > 0.85 and MAF > 0 based on an analysis of 260 trees.
^† Successful calls are those with a GenCall score ≥ 0.15 [19].
^§ 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).

ISSN: 1471-2164