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 mr1804 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
vg0702524630 sf0702523631 7 2524630 4.15E-08 2.99E-06
vg1103330790 sf1103326693 11 3330790 6.33E-08 1.99E-07
vg0322105332 sf0322103839 3 22105332 1.50E-07 5.82E-07
vg0617262301 sf0617261304 6 17262301 5.81E-07 2.81E-06
vg0922304115 sf0922303634 9 22304115 7.99E-07 4.39E-06
vg0434375933 sf0434190827 4 34375933 3.94E-06 2.99E-06
vg0616723603 sf0616722605 6 16723603 5.43E-06 5.97E-06
vg1109007680 sf1109002293 11 9007680 NA 3.53E-06
vg1209224752 sf1209222161 12 9224752 NA 4.00E-06