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 mr1909 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
vg0205292202 sf0205292200 2 5292202 4.26E-22 4.63E-17
vg0131768366 sf0131767322 1 31768366 2.44E-11 NA
vg0131785830 sf0131784786 1 31785830 4.88E-11 NA
vg0142744866 sf0142743822 1 42744866 1.74E-09 NA
vg1117584893 sf1117118750 11 17584893 6.29E-09 4.70E-06
vg0205289081 sf0205289079 2 5289081 7.92E-09 2.04E-06
vg0207801637 sf0207801636 2 7801637 5.85E-06 NA