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 mr1139 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
vg0719049384 sf0719048391 7 19049384 1.38E-14 5.79E-14
vg0719056561 sf0719055568 7 19056561 1.03E-13 3.85E-14
vg1213355825 sf1213353163 12 13355825 1.10E-06 2.66E-06
vg0329561125 sf0329554165 3 29561125 2.87E-06 1.88E-06
vg0719006525 sf0719005532 7 19006525 3.54E-06 2.51E-08
vg0128824887 sf0128823842 1 28824887 9.78E-06 NA
vg0816277234 sf0816274520 8 16277234 NA 4.39E-06