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 mr1759 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
vg1117583959 sf1117117816 11 17583959 3.64E-08 NA
vg0132204145 sf0132203101 1 32204145 2.15E-07 5.00E-06
vg0527829822 sf0527767179 5 27829822 5.52E-07 6.17E-06
vg0522014819 sf0521952261 5 22014819 4.96E-06 NA
vg0603938312 sf0603937313 6 3938312 8.21E-06 NA
vg0808453559 sf0808452563 8 8453559 8.85E-06 4.94E-06