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 mr1718 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
vg0321134351 sf0321132861 3 21134351 3.23E-102 1.16E-16
vg0321287375 sf0321285885 3 21287375 2.04E-100 9.54E-20
vg0317723555 sf0317722337 3 17723555 7.42E-96 2.30E-13
vg0317721273 sf0317720055 3 17721273 9.74E-96 2.21E-13
vg0324228407 sf0324226486 3 24228407 3.29E-94 2.20E-06
vg0523158351 sf0523095792 5 23158351 3.32E-93 9.06E-08
vg0324408073 sf0324406152 3 24408073 7.09E-93 2.22E-07
vg0522272712 sf0522210153 5 22272712 2.17E-92 2.38E-08
vg0717004818 sf0717003825 7 17004818 1.38E-87 4.65E-08
vg0717178130 sf0717177137 7 17178130 1.27E-80 5.21E-07
vg1017699353 sf1017628126 10 17699353 NA 4.83E-07
vg0630658313 sf0630657315 6 30658313 NA 1.00E-06
vg0419769666 sf0419597701 4 19769666 NA 1.04E-06
vg0407538739 sf0407534009 4 7538739 NA 1.96E-06
vg0611297427 sf0611296428 6 11297427 NA 2.25E-06
vg0308103910 sf0308102848 3 8103910 NA 2.31E-06
vg0100096616 sf0100095616 1 96616 NA 2.81E-06
vg0100100017 sf0100099017 1 100017 NA 3.18E-06
vg0308212271 sf0308211209 3 8212271 NA 3.47E-06