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 mr1777 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
vg0405832157 sf0405827596 4 5832157 8.90E-10 1.53E-06
vg0420146692 sf0419974732 4 20146692 3.83E-08 NA
vg0909378423 sf0909377422 9 9378423 3.88E-08 NA
vg1106628056 sf1106623809 11 6628056 4.79E-08 NA
vg0329021958 sf0329015010 3 29021958 5.66E-08 NA
vg0402131778 sf0402127373 4 2131778 1.82E-06 2.62E-06
vg0406864964 sf0406860409 4 6864964 5.41E-06 4.02E-06
vg0406871429 sf0406866874 4 6871429 NA 4.41E-07