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 mr1966 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
vg0303248763 sf0303247759 3 3248763 4.40E-07 4.40E-07
vg0406818237 sf0406813682 4 6818237 5.16E-07 5.17E-07
vg1120996498 sf1120530377 11 20996498 5.89E-07 5.89E-07
vg1126641326 sf1126169741 11 26641326 1.52E-06 1.52E-06
vg1222577056 sf1222543495 12 22577056 1.84E-06 1.84E-06
vg0129458284 sf0129457239 1 29458284 2.19E-06 2.19E-06
vg1106565379 sf1106561132 11 6565379 2.25E-06 2.25E-06
vg0429184263 sf0428999123 4 29184263 2.29E-06 2.29E-06
vg1120950747 sf1120484650 11 20950747 2.42E-06 2.43E-06
vg0900360701 sf0900359701 9 360701 3.39E-06 3.39E-06
vg0916047534 sf0916046533 9 16047534 3.91E-06 3.91E-06
vg0119798012 sf0119796967 1 19798012 4.40E-06 4.40E-06
vg1218169300 sf1218140736 12 18169300 4.63E-06 4.63E-06
vg0828075962 sf0828073248 8 28075962 4.83E-06 4.83E-06