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 mr1971 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
vg0610849825 sf0610848826 6 10849825 3.22E-27 3.88E-08
vg0616175231 sf0616174233 6 16175231 2.50E-26 NA
vg0620989288 sf0620988291 6 20989288 4.13E-26 NA
vg0526175307 sf0526112727 5 26175307 8.74E-26 NA
vg0306336761 sf0306335761 3 6336761 3.52E-25 NA
vg0620630387 sf0620629390 6 20630387 3.69E-24 1.51E-06
vg0614795778 sf0614794779 6 14795778 8.56E-24 1.07E-06
vg0141744070 sf0141743027 1 41744070 7.55E-22 9.34E-06
vg0610367772 sf0610366773 6 10367772 NA 2.14E-08
vg1001249422 sf1001248399 10 1249422 NA 5.18E-07
vg0611438317 sf0611437318 6 11438317 NA 1.87E-06
vg0610443754 sf0610442755 6 10443754 NA 3.45E-06
vg0225867144 sf0225861275 2 25867144 NA 4.82E-06
vg1219459084 sf1219430554 12 19459084 NA 4.85E-06