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 mr1994 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
vg1122387797 sf1121921668 11 22387797 3.71E-10 NA
vg0913007991 sf0913006990 9 13007991 2.97E-09 NA
vg0123800663 sf0123799619 1 23800663 2.25E-08 NA
vg0234966017 sf0234960148 2 34966017 4.39E-08 NA
vg0113344604 sf0113343578 1 13344604 4.42E-08 NA
vg0133032292 sf0133031248 1 33032292 1.07E-07 NA
vg0227089280 sf0227083411 2 27089280 5.96E-07 1.76E-06
vg0122291977 sf0122290932 1 22291977 1.58E-06 NA
vg0906299067 sf0906298067 9 6299067 NA 1.21E-06
vg1128896330 sf1128373109 11 28896330 NA 1.42E-06
vg1125281160 sf1124815000 11 25281160 NA 4.49E-06
vg0200805132 sf0200805132 2 805132 NA 6.34E-06