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 mr1855 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
vg1215632569 sf1215629866 12 15632569 2.87E-08 4.08E-06
vg1125171325 sf1124705165 11 25171325 6.27E-08 5.54E-07
vg0819245930 sf0819243217 8 19245930 3.61E-07 6.92E-06
vg0906784569 sf0906783569 9 6784569 4.50E-07 3.65E-06
vg0407096672 sf0407091942 4 7096672 5.17E-07 4.83E-08
vg0529703228 sf0529640583 5 29703228 1.06E-06 NA
vg0432240299 sf0432055192 4 32240299 1.39E-06 2.76E-06
vg0401709901 sf0401705450 4 1709901 2.77E-06 2.39E-06
vg0401708881 sf0401704430 4 1708881 9.55E-06 NA