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

Table 2 Summary of the in silico SNP development procedure using increasingly stringent SNP selection and design requirements (F0 through F4) (see methods for details)

In silico SNP performance assessment	F0	F1	F2	F3	F4
# of SNPs	66,254	21,944	10,032	3,187	1,329
# of contigs with SNPs	9,579	5,058	2,057	1,651	998
# of SNPs submitted to the ADT	621	605	583	367	547
# of SNPs with ADT Score ≥ 0.6	598	572	557	353	525
% of SNPs with ADT Score ≥ 0.6	96.3	94.5	95.5	96.2	96.0
# of SNPs with ADT Score ≥ 0.9	314	316	297	177	291
% of SNPs with ADT Score ≥ 0.9	50.6	52.2	50.9	48.2	53.2
# of SNPs tested by the GGGT	96	96	108	108	288

ISSN: 1471-2229