Table 2.

Information about unimputed SNPs detected in eight maize 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	267	242	955,120	167,617	1.42	0.92	54.60	32.73	0.22	0.83	0.09	0.23
Pop2	523	513	955,120	115,311	1.46	0.78	60.83	33.48	0.11	0.56	0.09	0.24
Pop3	174	161	45,098	40,491	2.32	1.97	23.56	20.37	9.50	10.50	0.25	0.25
Pop4	152	152	41,307	13,662	1.88	1.22	57.44	31.85	5.46	12.68	0.27	0.27
Pop5	411	408	66,725	57,411	2.42	2.31	24.74	18.99	20.23	23.17	0.43	0.43
Pop6	207	177	65,814	48,985	2.73	1.99	21.03	16.36	0.86	0.87	0.35	0.43
Pop7	207	185	75,961	19,089	1.32	0.57	57.96	34.88	0.68	1.56	0.41	0.44
Pop8	285	216	73,013	36,468	1.26	0.88	49.55	36.13	0.70	1.00	0.40	0.42

^aPercentage of missing SNP.

^bPercentage of heterozygous SNP.

^cMinor allele frequency.