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 mr1996 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
vg0123470105 sf0123469061 1 23470105 1.40E-07 1.40E-07
vg0221212277 sf0221206409 2 21212277 4.57E-07 4.58E-07
vg0122407829 sf0122406784 1 22407829 4.69E-07 4.70E-07
vg0233935333 sf0233929464 2 33935333 4.94E-07 4.94E-07
vg1014198395 sf1014127161 10 14198395 6.33E-07 6.33E-07
vg0122381459 sf0122380414 1 22381459 2.03E-06 2.03E-06
vg1117240580 sf1116774432 11 17240580 2.32E-06 2.32E-06
vg0307489962 sf0307488900 3 7489962 2.56E-06 2.56E-06
vg0719581422 sf0719580429 7 19581422 4.45E-06 4.46E-06