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 mr1638 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
vg1104128457 sf1104124359 11 4128457 2.55E-69 2.59E-28
vg0200779191 sf0200779191 2 779191 7.75E-34 NA
vg0805425070 sf0805424073 8 5425070 8.21E-34 NA
vg0321319909 sf0321318419 3 21319909 2.59E-33 NA
vg0729559113 sf0729558121 7 29559113 5.66E-33 NA
vg1104136577 sf1104132479 11 4136577 NA 1.61E-12
vg1104300143 sf1104296045 11 4300143 NA 2.31E-06