Table 3:

Summary of SNP counts by reference genome and concordant SNPs with the 90K SNP buffalo genotyping array. Only the SNPs aligned with UOA_WB_1 were used to determine concordant SNPs in the 90K SNP buffalo genotyping array. Description for the SNPs rows was as follows: All = all SNPs found without filtering; Autosomes only = all SNPs found in the autosomes without another filtering; Swamp after QC = SNPs identified in swamp buffalo animals after quality filtering; River after QC = SNPs identified in river buffalo animals after quality filtering; Swamp specific = SNPs identified only in the swamp (not in river) buffalo animals after quality filtering; River specific = SNPs identified only in the river (not in swamp) buffalo animals after quality filtering; River and swamp shared = SNPs identified in both river and swamp buffalo animals after quality filtering

SNPs	PCC_UOA_SB_1v2	UOA_WB_1	90K SNP buffalo array
All	41,632,997	41,071,165	90,000
Autosomes only	40,905,045	40,340,557	72,434
Swamp after QC	22,847,574	24,914,052	39,278
River after QC	26,525,477	24,485,667	65,890
Swamp specific	10,161,461	11,756,460	278
River specific	13,839,364	11,328,075	26,890
River and swamp shared	12,686,113	13,157,592	39,000