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 mr1460 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
vg0514534980 sf0514477523 5 14534980 1.30E-09 1.30E-09
vg0219335600 sf0219329732 2 19335600 1.79E-07 1.79E-07
vg0514439240 sf0514381783 5 14439240 3.76E-07 3.76E-07
vg0510163595 sf0510163524 5 10163595 4.74E-07 4.74E-07
vg0510329960 sf0510329889 5 10329960 7.39E-07 7.39E-07
vg0728044654 sf0728043661 7 28044654 9.29E-07 9.30E-07
vg0728021019 sf0728020026 7 28021019 1.30E-06 1.30E-06
vg0210325233 sf0210325231 2 10325233 1.84E-06 1.84E-06
vg0727093350 sf0727092356 7 27093350 2.46E-06 2.46E-06
vg1221014609 sf1220981159 12 21014609 2.67E-06 2.67E-06
vg0728022403 sf0728021410 7 28022403 3.11E-06 3.11E-06