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 mr1224 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
vg0719048035 sf0719047042 7 19048035 8.17E-19 7.87E-15
vg1107674285 sf1107670030 11 7674285 1.77E-10 3.50E-07
vg0317247798 sf0317246608 3 17247798 1.93E-08 NA
vg0101822336 sf0101821336 1 1822336 4.57E-08 NA
vg0710180880 sf0710179886 7 10180880 4.65E-08 NA
vg1220167325 sf1220138767 12 20167325 3.31E-07 4.07E-06
vg0819246479 sf0819243766 8 19246479 9.14E-06 1.88E-06