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 mr1360 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
vg1103571301 sf1103567204 11 3571301 6.89E-12 5.05E-06
vg0405708665 sf0405704104 4 5708665 1.88E-11 3.46E-06
vg0139781249 sf0139780206 1 39781249 3.10E-10 NA
vg1103096800 sf1103092703 11 3096800 4.89E-10 1.38E-06
vg0124035433 sf0124034389 1 24035433 9.42E-10 NA
vg0701450700 sf0701449700 7 1450700 9.83E-10 NA
vg1217795967 sf1217767401 12 17795967 5.88E-08 3.31E-07
vg0224679378 sf0224673509 2 24679378 2.51E-06 3.88E-06