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

BMC Genomics

Table 7 Douglas-fir SNPs detected using an Illumina Infinium SNP array (n = 260 trees)

		No. of SNPs in category/No. of SNPs attempted or assayed (%)^*
SNP category	Number of SNPs	Attempted (n=8769)	Assayed (n=8067)
SNPs attempted	8769	100.0	108.7
SNPs assayed	8067	92.0	100.0
Called SNPs (call frequency > 0.85)^†	7256	82.7	89.9
Called SNPs that are polymorphic (MAF > 0)	5847	66.7	72.5
Percent of called SNPs that are polymorphic (5847/7256) = 80.6

^*The number of SNPs in each category is expressed as a percentage of the total number of SNPs attempted (n = 8769) and number of SNPs successfully assayed on the array (n = 8067).
^†Successful calls are those with a GenCall score ≥ 0.15 [19].

ISSN: 1471-2164