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Table 2 Top ten SNPs with significantly different allele frequencies among different germplasm origins

From: Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines

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
  1. Chr = chromosome.