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 mr1239 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
vg0412697867 sf0412688578 4 12697867 7.89E-18 NA
vg0122837670 sf0122836626 1 22837670 6.01E-17 NA
vg0222863832 sf0222857963 2 22863832 8.93E-17 NA
vg0133978114 sf0133977070 1 33978114 1.10E-16 NA
vg0131382321 sf0131381277 1 31382321 4.24E-16 NA
vg0405898738 sf0405894179 4 5898738 9.44E-13 3.56E-06
vg1108112165 sf1108107910 11 8112165 NA 3.07E-06