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 mr1531 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
vg0314648455 sf0314647142 3 14648455 7.65E-09 NA
vg1123553400 sf1123087270 11 23553400 1.17E-08 NA
vg0208134492 sf0208134491 2 8134492 1.55E-08 NA
vg0431811870 sf0431626763 4 31811870 1.64E-08 NA
vg0422251052 sf0422065934 4 22251052 2.12E-08 NA
vg1125834367 sf1125368286 11 25834367 8.74E-07 5.65E-06
vg0316216814 sf0316215462 3 16216814 4.57E-06 NA