Table 3.

Imputed SNP information for eight populations before and after data filtering.

Pop	Number of taxa		SNPs		Insertion/deletion (%)		Missing (%)a		Het (%)b		MAFc
	Unfiltered	Filtered	Unfiltered	Filtered	Unfiltered	Filtered	Unfiltered	Filtered	Unfiltered	Filtered	Unfiltered	Filtered
Pop1	242	242	955,120	341,312	0.82	0.62	15.20	12.75	0.94	2.30	0.09	0.23
Pop2	513	513	955,120	340,177	0.92	0.47	13.49	12.17	0.64	1.58	0.09	0.24
Pop3	161	161	93,760	76,437	1.48	0.74	8.44	2.86	19.40	21.26	0.24	0.24
Pop4	152	152	92,752	90,655	0.95	0.66	9.02	7.91	34.18	34.41	0.24	0.25
Pop5	408	408	91,564	90,637	1.88	1.74	4.07	3.66	43.10	43.67	0.45	0.45
Pop6	177	177	91,208	74,487	1.38	1.73	2.89	1.94	0.78	0.91	0.35	0.43
Pop7	185	185	121,935	121,013	1.78	0.71	2.45	2.11	5.36	5.39	0.45	0.45
Pop8	216	216	111,568	110,422	1.02	0.76	4.17	3.84	2.78	2.80	0.42	0.42

^aPercentage of missing SNP.

^bPercentage of heterozygous SNP.

^cMinor allele frequency.