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 mr1989 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
vg0523509598 sf0523447019 5 23509598 3.35E-11 NA
vg0517793133 sf0517732619 5 17793133 4.31E-11 NA
vg0812039331 sf0812038336 8 12039331 6.61E-11 NA
vg0202909303 sf0202909301 2 2909303 6.82E-11 NA
vg0402373904 sf0402369499 4 2373904 7.94E-11 NA
vg0820796179 sf0820793466 8 20796179 1.14E-10 1.43E-06
vg0431561696 sf0431376592 4 31561696 1.65E-08 NA
vg0128646920 sf0128645875 1 28646920 3.40E-08 NA
vg0608826344 sf0608825345 6 8826344 2.02E-07 NA
vg0529442914 sf0529380269 5 29442914 NA 2.84E-07
vg0407766368 sf0407761636 4 7766368 NA 2.43E-06