Table 2.

Top ten SNPs with significantly different allele frequencies among different germplasm origins

SNP number	SNP name	chr	Position	Allele	Allele frequency		Allele frequency difference
					I	II
INERA (I) versus Temperate (II)
54	PZB01062.3	1	56846728	A	0.25	0.8	0.55
70	PHM12633.15	1	1.03E + 08	A	0.99	0.4	0.59
187	PZA00172.12	2	4177515	A	0.14	0.8	0.66
245	PZA00637.6	2	1.7E + 08	A	0.35	0.95	0.6
282	PZA01352.5	2	2.26E + 08	A	0.86	0.15	0.71
310	PZA00297.2	3	39992968	C	0.24	0.78	0.54
594	PZA00643.13	5	91096945	G	0.91	0.2	0.71
779	PZA02854.13	7	1.38E + 08	A	0.32	0.9	0.58
902	PHM11946.19	9	9886093	A	0.26	0.9	0.64
INERA (I) versus CIMMYT (II)
234	PZA01537.2	2	1.51E + 08	A	0.78	0.27	0.51
254	PZA00824.2	2	1.94E + 08	A	0.92	0.43	0.5
498	PZA02479.1	4	2.18E + 08	A	0.57	0.09	0.48
628	PHM532.23	5	1.93E + 08	A	0.98	0.47	0.51
671	PHM2551.31	6	85125455	A	0.68	0.2	0.48
689	PZA01591.1	6	1.25E + 08	A	0.08	0.57	0.49
871	PHM12749.13	8	1.55E + 08	C	0.12	0.59	0.48
876	PZA00838.2	8	1.59E + 08	A	0.15	0.67	0.51
1034	PZA01073.1	10	1.45E + 08	A	0.36	0.93	0.57
1046	PZA00311.5	-	-	A	0.08	0.59	0.51
INERA (I) versus IITA (II)
344	PZB02179.1	3	1.58E + 08	A	0.8	0.27	0.53
404	PHM2423.33	3	2.28E + 08	A	0.25	0.85	0.6
469	PZA03116.1	4	1.66E + 08	A	0.71	0.17	0.54
522	PZA01887.1	5	656148	A	0.05	0.6	0.55
865	PZB01454.1	8	1.46E + 08	A	0.19	0.75	0.56
998	PZB00409.1	10	84002430	A	0.13	0.69	0.56
1002	PZA02398.2	10	99471436	A	0.06	0.73	0.67
1033	PHM5435.25	10	1.44E + 08	A	0.25	0.82	0.57
1036	PZA01001.2	10	1.47E + 08	A	0.33	0.86	0.53
1055	PZA02474.1	-	-	A	0.69	0.07	0.62

Chr = chromosome.