Table 2

Success rate. Success rate obtained over 768 SNPs assayed for each of white spruce and black spruce using the GoldenGate SNP assay. Numbers in parentheses are the percentages obtained by using as a reference the total of 768 SNPs assayed per species or the total number of genes assayed.

On a SNP basis

On a gene basis


Number of SNPs assayed

Number of SNPs with GenTrain score ≥ 0.25 2

Number of segregating SNPs with GenTrain score ≥ 0.25 2

Number of monomorphic SNPs with GenTrain score ≥ 0.25 2

Number of genes assayed

Number of segregating genes


White spruce

Resequenced SNPs

730 (95%)

596 (81.6%)

505 (69.2%)

62 (8.5%)

in silico SNPs 1

38 (5%)

31 (81.6%)

11 (28.9%)

25 (65.8%)

Total

768 (100%)

603 (78.5%)

516 (67.2%)

87 (11.3%)

425

330 (77.6%)

Black spruce

Resequenced SNPs

768 (100%)

630 (82.0%)

592 (77.1%)

31 (4.0%)

348

311 (89.4%)


1 in silico SNPs were detected in aligned EST derived from white spruce cDNA libraries. The resource is described in Pavy et al. [18]. For black spruce, all SNPs were obtained after resequencing from genomic DNA.

2 For SNPs with a GenTrain score ≥ 0.25, valid GenCall scores were obtained for 99.4% of samples, on average (see Results).

Pavy et al. BMC Genomics 2008 9:21   doi:10.1186/1471-2164-9-21

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