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 mr1862 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
vg1018510396 sf1018438953 10 18510396 2.74E-34 2.74E-08
vg1018432054 sf1018360611 10 18432054 3.34E-33 1.61E-10
vg0729456166 sf0729455174 7 29456166 4.39E-28 NA
vg0516323967 sf0516266449 5 16323967 2.07E-27 NA
vg0310381006 sf0310379922 3 10381006 3.17E-27 NA
vg0128089631 sf0128088587 1 28089631 1.06E-26 NA
vg1126138571 sf1125666985 11 26138571 NA 9.69E-08
vg1126171702 sf1125700116 11 26171702 NA 1.97E-07
vg0432426919 sf0432241810 4 32426919 NA 1.17E-06
vg0432446360 sf0432261252 4 32446360 NA 1.49E-06
vg1116968421 sf1116503299 11 16968421 NA 1.58E-06