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 mr1496 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
vg0222673217 sf0222667348 2 22673217 1.41E-45 6.29E-28
vg0222675535 sf0222669666 2 22675535 2.78E-44 1.11E-29
vg0222739148 sf0222733279 2 22739148 1.38E-30 1.25E-27
vg0110304750 sf0110303726 1 10304750 1.23E-20 3.64E-07
vg0518201525 sf0518141011 5 18201525 3.29E-20 3.15E-07
vg0507023861 sf0507023803 5 7023861 3.43E-20 NA
vg0526731344 sf0526668702 5 26731344 3.54E-20 1.93E-07
vg0516812952 sf0516752593 5 16812952 8.98E-20 1.43E-08
vg0518620627 sf0518558110 5 18620627 3.05E-19 8.86E-09
vg0222988287 sf0222982418 2 22988287 3.89E-19 2.17E-09
vg0505887711 sf0505887649 5 5887711 1.41E-18 3.01E-08
vg1110425815 sf1110420360 11 10425815 2.60E-18 1.22E-08
vg0825750246 sf0825747532 8 25750246 3.30E-18 2.00E-08
vg0306047262 sf0306046262 3 6047262 7.29E-18 5.51E-09
vg0500664660 sf0500664660 5 664660 2.22E-16 1.35E-09
vg0922708358 sf0922707877 9 22708358 4.20E-16 1.93E-08
vg0222952563 sf0222946694 2 22952563 2.70E-15 3.40E-12
vg1204507349 sf1204506337 12 4507349 3.22E-14 3.69E-08
vg0141576432 sf0141575389 1 41576432 3.87E-14 5.61E-08
vg0121803138 sf0121802093 1 21803138 4.20E-14 1.57E-08
vg0616706040 sf0616705042 6 16706040 5.27E-13 5.08E-09
vg0222722554 sf0222716685 2 22722554 NA 2.16E-15
vg0327037726 sf0327030779 3 27037726 NA 1.37E-09
vg0222926098 sf0222920229 2 22926098 NA 2.58E-09
vg1016340773 sf1016269549 10 16340773 NA 3.23E-09
vg0222271516 sf0222265647 2 22271516 NA 3.71E-08
vg0626215270 sf0626214273 6 26215270 NA 3.90E-08
vg0709837237 sf0709836243 7 9837237 NA 3.98E-08
vg0506223844 sf0506223783 5 6223844 NA 5.41E-08
vg0401716915 sf0401712464 4 1716915 NA 1.17E-07
vg0421291212 sf0421119266 4 21291212 NA 2.00E-07
vg0311437556 sf0311436274 3 11437556 NA 2.95E-07
vg0811720061 sf0811719066 8 11720061 NA 6.26E-06