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 mr1339 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
vg1219164957 sf1219136391 12 19164957 5.72E-08 1.18E-06
vg0402103921 sf0402099515 4 2103921 9.61E-07 3.79E-06
vg1214331148 sf1214328488 12 14331148 1.54E-06 4.84E-06
vg0525305598 sf0525243019 5 25305598 1.73E-06 2.20E-06
vg1127789167 sf1127317553 11 27789167 2.81E-06 2.03E-06
vg0420837344 sf0420665387 4 20837344 4.05E-06 6.39E-07
vg0702621393 sf0702620394 7 2621393 NA 4.17E-06