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 mr1650 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
vg0803654150 sf0803653153 8 3654150 2.76E-18 1.06E-10
vg0402180792 sf0402176387 4 2180792 1.77E-17 4.43E-08
vg0401968013 sf0401963609 4 1968013 4.66E-17 1.23E-08
vg0724248089 sf0724247095 7 24248089 1.00E-16 9.26E-07
vg0618798718 sf0618797721 6 18798718 3.69E-16 5.26E-09
vg0725411074 sf0725410080 7 25411074 6.09E-16 4.80E-07
vg0133884657 sf0133883613 1 33884657 6.98E-16 2.49E-09
vg0919855604 sf0919855123 9 19855604 1.96E-15 2.83E-07
vg0134272325 sf0134271282 1 34272325 2.42E-15 1.38E-09
vg0409634255 sf0409624953 4 9634255 2.69E-15 7.19E-07
vg0137195833 sf0137194790 1 37195833 5.11E-15 1.67E-07
vg0612100813 sf0612099814 6 12100813 7.67E-15 1.40E-06
vg0120417176 sf0120416131 1 20417176 8.08E-15 3.37E-07
vg0113480569 sf0113479543 1 13480569 8.17E-15 8.71E-07
vg0626321316 sf0626320319 6 26321316 1.48E-14 2.09E-06
vg0405387818 sf0405383259 4 5387818 2.35E-14 2.52E-06
vg1226817020 sf1226783419 12 26817020 5.58E-14 3.08E-07
vg0412751761 sf0412742471 4 12751761 5.60E-14 4.91E-06
vg0604882318 sf0604881319 6 4882318 1.39E-13 3.57E-06
vg0408433193 sf0408428467 4 8433193 1.60E-13 8.32E-06
vg0618517599 sf0618516602 6 18517599 7.89E-13 6.36E-07
vg0433794465 sf0433609350 4 33794465 1.01E-12 4.27E-06
vg0803657241 sf0803656244 8 3657241 NA 5.41E-09
vg0219044073 sf0219038205 2 19044073 NA 1.28E-06
vg0401249964 sf0401245514 4 1249964 NA 2.23E-06
vg0219199169 sf0219193301 2 19199169 NA 2.52E-06
vg0622678034 sf0622677037 6 22678034 NA 2.53E-06
vg1105347465 sf1105343216 11 5347465 NA 4.59E-06