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 mr1160 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
vg1224027002 sf1223993455 12 24027002 1.59E-07 1.59E-07
vg0404528034 sf0404523637 4 4528034 2.86E-07 2.86E-07
vg0919038342 sf0919037342 9 19038342 3.40E-07 3.40E-07
vg1122051014 sf1121584885 11 22051014 1.82E-06 1.82E-06
vg0921058093 sf0921057612 9 21058093 2.74E-06 2.74E-06
vg0511247093 sf0511247022 5 11247093 4.00E-06 4.00E-06
vg0208608994 sf0208608993 2 8608994 4.43E-06 4.42E-06