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 mr1333 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
vg0101041880 sf0101040880 1 1041880 2.63E-08 NA
vg0423982013 sf0423796871 4 23982013 6.76E-08 NA
vg0808721437 sf0808720441 8 8721437 3.24E-07 1.11E-06
vg0201664747 sf0201664747 2 1664747 3.00E-06 1.82E-06
vg0112635655 sf0112634629 1 12635655 3.25E-06 NA
vg0133436043 sf0133434999 1 33436043 6.65E-06 1.56E-06
vg0625839941 sf0625838944 6 25839941 NA 4.16E-06