Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1390 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1215965939 sf1215963235 12 15965939 8.20E-168 1.01E-58
vg1215968758 sf1215966054 12 15968758 5.53E-165 3.79E-59
vg1210219854 sf1210217266 12 10219854 8.20E-83 NA
vg1224007541 sf1223973994 12 24007541 5.91E-70 NA
vg0217071443 sf0217065573 2 17071443 7.55E-65 NA
vg1210306695 sf1210304108 12 10306695 2.00E-64 4.79E-07
vg1213439429 sf1213436767 12 13439429 9.47E-62 NA
vg1212938220 sf1212935559 12 12938220 5.69E-60 6.63E-07
vg1215871396 sf1215868692 12 15871396 NA 1.71E-28
vg1215969757 sf1215967053 12 15969757 NA 1.11E-13
vg1215871822 sf1215869118 12 15871822 NA 1.13E-13
vg0610620315 sf0610619316 6 10620315 NA 1.19E-08
vg1216151755 sf1216149051 12 16151755 NA 1.50E-08
vg1215962650 sf1215959946 12 15962650 NA 1.85E-08
vg1216278472 sf1216275768 12 16278472 NA 7.91E-08
vg1216535261 sf1216532554 12 16535261 NA 8.13E-08
vg1018220310 sf1018148869 10 18220310 NA 1.69E-07
vg1216469931 sf1216467224 12 16469931 NA 2.30E-07
vg1216413575 sf1216410868 12 16413575 NA 3.11E-07
vg1215763538 sf1215760835 12 15763538 NA 3.90E-07
vg1215261373 sf1215258671 12 15261373 NA 4.40E-07
vg1223876846 sf1223843299 12 23876846 NA 7.67E-07
vg1104366840 sf1104362742 11 4366840 NA 8.67E-07
vg0401349008 sf0401344558 4 1349008 NA 1.41E-06
vg1005031656 sf1005048193 10 5031656 NA 2.52E-06
vg0710900579 sf0710899585 7 10900579 NA 2.77E-06