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 mr1584 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
vg1019686736 sf1019615237 10 19686736 6.46E-26 5.51E-06
vg1019995139 sf1019923638 10 19995139 1.39E-25 1.95E-06
vg0310549448 sf0310548364 3 10549448 2.09E-25 6.58E-06
vg1217106249 sf1217100204 12 17106249 4.67E-25 2.84E-06
vg0130051624 sf0130050579 1 30051624 3.38E-24 NA
vg0104403637 sf0104402637 1 4403637 5.70E-24 NA
vg0413759612 sf0413750326 4 13759612 NA 6.23E-08
vg1008380500 sf1008309362 10 8380500 NA 1.49E-06
vg0414193101 sf0414183817 4 14193101 NA 1.85E-06
vg0414062987 sf0414053702 4 14062987 NA 3.01E-06
vg1201535604 sf1201534604 12 1535604 NA 4.41E-06
vg0719955551 sf0719954558 7 19955551 NA 4.80E-06