Table 2.

Total number, density, minor allele frequency and heterozygosity of the filtered variants generated by different GBS pipelines.

Pipeline	Number of variants	Site depth	Site missing	MAF	Hetero-zygosity	% heter ≥ 0.5
FreeBayes	10,403	1.3	0.28	0.11	0.19	0.5
TASSEL	24,176	8.8	0.31	0.32	0.43	35
UNEAK	14,415	3.5	0.5	0.22	0.39	28

MAF, minor allele frequency; % heter ≥ 0.5, percentage of heterozygosity equal or more than 0.5.