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 mr1992 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
vg0314748691 sf0314747378 3 14748691 4.39E-07 4.39E-07
vg1002823994 sf1002822971 10 2823994 1.56E-06 1.56E-06
vg1122356822 sf1121890693 11 22356822 2.80E-06 2.80E-06
vg1010157820 sf1010086641 10 10157820 4.14E-06 4.14E-06
vg0229389860 sf0229383991 2 29389860 4.79E-06 4.79E-06