Table 3. Counts of putative loci after different filtering steps.

Filtering No.	Feature	Value
	Total number of SNPs	1,184,075
i	Bi-allelic SNPs	1,166,783
ii	SNPs with quality score > 20	1,052,835
iii	The average depth of reads > 4 and < 100 and > 80% coverage for each population	109,307
iv	A global minor allele frequency (MAF ≥ 0.05) in two populations	64,008
v	HO < 0.5 and -0.3 < FIS < 0.3 per SNP for each population	42,733
vi	One SNP per contig	22, 648 (S3 File)