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 mr1488 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
vg0209482698 sf0209482696 2 9482698 1.00E-06 1.00E-06
vg0118124341 sf0118123295 1 18124341 2.20E-06 2.20E-06
vg1010118291 sf1010047112 10 10118291 2.51E-06 2.51E-06
vg0728388703 sf0728387711 7 28388703 4.68E-06 4.68E-06
vg1009009289 sf1008938150 10 9009289 8.52E-06 8.52E-06