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Table 3 SNPs associated with the defense response at fdr p-value <0.10

From: Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil

GAPIT/CMLM
SNP Chromo Position Alleles MAF p-value FDR p-value R2 Allelic Effect
S18_14,327,556* 18 14,327,556 T/C 0.491349481 2.23E-05 0.0751889 4.41% 0.81844
S18_14,327,607 18 14,327,607 A/G 0.493079585 3.86E-05 0.0751889 4.15% −0.79800
S1_36,783,951 1 36,783,951 G/A 0.264705882 5.50E-05 0.0751889 3.98% 0.65452
S1_36,497,505 1 36,497,505 A/G 0.269896194 6.33E-05 0.0751889 3.91% −0.63779
S1_35,474,053 1 35,474,053 C/T 0.261245675 9.03E-05 0.0751889 3.75% −0.62749
S11_6,493,121* 11 6,493,121 T/C 0.228373702 9.48E-05 0.0751889 3.72% −0.58271
S1_35,045,463 1 35,045,463 C/T 0.26816609 1.03E-04 0.0751889 3.69% −0.62200
S1_36,006,734 1 36,006,734 A/G 0.271626298 1.06E-04 0.0751889 3.67% −0.60778
S18_14,517,407 18 14,517,407 C/A 0.489619377 1.17E-04 0.0751889 3.62% 0.74685
S18_14,517,362 18 14,517,362 C/T 0.489619377 1.17E-04 0.0751889 3.62% −0.74685
S1_36,045,483* 1 36,045,483 G/A 0.262975779 1.81E-04 0.0878468 3.42% 0.58989
S18_14,282,760 18 14,282,760 A/G 0.496539792 1.97E-04 0.0878468 3.38% 0.72465
S18_14,282,812 18 14,282,812 A/G 0.496539792 1.97E-04 0.0878468 3.38% 0.72465
S18_14,282,806 18 14,282,806 T/C 0.496539792 1.97E-04 0.0878468 3.38% −0.72465
S1_35,152,187 1 35,152,187 T/G 0.271626298 2.09E-04 0.0878468 3.35% 0.59070
S19_1,289,850 19 1,289,850 A/G 0.155709343 2.25E-04 0.0878468 3.32% −0.61268
S18_14,324,249 18 14,324,249 G/T 0.496539792 2.46E-04 0.0878468 3.27% 0.71140
S18_14,324,245 18 14,324,245 T/C 0.496539792 2.46E-04 0.0878468 3.27% −0.71140
S18_14,334,212 18 14,334,212 T/C 0.5 2.86E-04 0.0968226 3.20% −0.69934
FarmCPU
SNP Chromo Position Alleles MAF p-value FDR p-val R2 Allelic Effect
S18_14,327,556* 18 14,327,556 T/C 0.491349481 1.54E-07 0.0009911 3.26% 0.64476
S11_6,493,121* 11 6,493,121 T/C 0.228373702 2.48E-06 0.0079806 2.44% −0.41685
S1_36,045,483* 1 36,045,483 G/A 0.262975779 5.38E-06 0.0115419 2.29% 0.40215
S9_32,113,409 9 32,113,409 C/T 0.335640138 7.51E-06 0.0120836 2.25% 0.34200
S4_7,210,961 4 7,210,961 C/G 0.249134948 9.64E-06 0.0124086 2.27% 0.38084
S16_3,111,366 16 3,111,366 G/A 0.14532872 1.50E-05 0.0160900 2.09% −0.46977
  1. * SPNs marked were significant by both GAPIT/CMLM and FarmCPU