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 mr1591 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
vg0331832899 sf0331825776 3 31832899 1.35E-07 1.35E-07
vg0139299500 sf0139298457 1 39299500 3.07E-07 3.07E-07
vg0203591903 sf0203591900 2 3591903 2.41E-06 2.41E-06
vg0813434555 sf0813432108 8 13434555 2.75E-06 2.75E-06
vg0216897057 sf0216891187 2 16897057 3.58E-06 3.58E-06
vg0816926894 sf0816924180 8 16926894 3.58E-06 3.58E-06
vg1005051336 sf1005067873 10 5051336 4.18E-06 4.18E-06