High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species.

filters F3+F4; 365 SNPs in 396) (Table 3 ), a highly significant difference was found in the final number of SNPs recovered with call rates ≥ 95%, (Chi-square Pearson = 17.40; p = 0.00003).

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The proportion of SNPs with call rates ≥ 95% varied, with an increasing trend when going toward a more stringent SNP filtering selection and reaching 93.1% with filter F4.

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When SNPs in these two classes were classified for polymorphism, a clear trend emerged indicating that a significantly larger proportion of SNPs called in silico by both PolyBayes and MIRA were in fact polymorphic in the GGGT assay when compared by those called exclusively by PolyBayes (p = 0.00024).

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