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 mr1487 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
vg0411212334 sf0411203035 4 11212334 8.85E-07 8.84E-07
vg0431750098 sf0431564990 4 31750098 2.63E-06 2.64E-06
vg0115958705 sf0115957679 1 15958705 4.00E-06 4.00E-06
vg0629767191 sf0629766193 6 29767191 4.69E-06 4.69E-06
vg1011517194 sf1011446013 10 11517194 7.16E-06 7.13E-06