Table 1.

Number of SNPs remaining after each filtering step.

Filtering Step	Targeted-GBS (tGBS) Method	Transcriptome-Based GBS (GBS-t) Method
Depth 5	2,043,680	1,614,141
Maximum missing 80 and Q30	457,692	90,493
Heterozygosity 0.2	450,927	85,641
Minor allelic frequency 0.05	57,344	53,186
Final analysis	56,349	52,471