TABLE 3.

Number of SNPs identified in genetic diversity and allele frequency-based genomic analysis.

	Phylogenetic tree construction	Allele-frequency-based analysis
Filtering step	No. of SNPs remaining after each filtering step
DP 5	12,522,726	11,099,596
Maximum missing 50% and Q30	1,414,996	1,345,992
MAF 0.05	422,101	563,692