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 mr1950 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
vg1010137144 sf1010065965 10 10137144 1.77E-07 1.77E-07
vg0711049866 sf0711048872 7 11049866 5.82E-07 5.82E-07
vg0401615936 sf0401611485 4 1615936 7.71E-07 7.71E-07
vg0127517746 sf0127516702 1 27517746 8.96E-07 8.96E-07
vg0315349538 sf0315348185 3 15349538 3.00E-06 3.00E-06
vg0324202574 sf0324200653 3 24202574 3.19E-06 3.19E-06
vg0419067732 sf0418895770 4 19067732 3.86E-06 3.86E-06
vg0205338762 sf0205338761 2 5338762 4.27E-06 4.27E-06
vg0205347525 sf0205347525 2 5347525 4.48E-06 4.48E-06
vg0803095828 sf0803094831 8 3095828 5.50E-06 5.50E-06