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 mr1921 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
vg0205296507 sf0205296506 2 5296507 3.33E-21 3.99E-16
vg1117584893 sf1117118750 11 17584893 7.08E-10 2.97E-06
vg0131768366 sf0131767322 1 31768366 2.29E-09 NA
vg0126085904 sf0126084860 1 26085904 1.66E-08 NA
vg1127791472 sf1127319858 11 27791472 2.06E-08 2.88E-06
vg0205289081 sf0205289079 2 5289081 2.09E-08 4.68E-06
vg0205099249 sf0205099246 2 5099249 2.51E-07 3.42E-06
vg1117158706 sf1116692558 11 17158706 7.67E-07 NA