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 mr1897 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
vg0217157408 sf0217151538 2 17157408 1.76E-12 7.07E-10
vg0217073423 sf0217067553 2 17073423 8.72E-12 1.05E-10
vg0805580015 sf0805579018 8 5580015 4.99E-10 3.33E-08
vg0319889987 sf0319888498 3 19889987 9.09E-09 4.91E-07
vg0216805204 sf0216799334 2 16805204 2.02E-08 7.12E-08
vg0317018800 sf0317017674 3 17018800 7.03E-08 1.81E-06
vg0103188289 sf0103187289 1 3188289 3.20E-07 2.79E-06
vg0208695804 sf0208695803 2 8695804 1.45E-06 2.68E-06