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 mr1714 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
vg0205952749 sf0205952749 2 5952749 8.41E-15 2.58E-07
vg0206499072 sf0206499072 2 6499072 3.28E-14 6.07E-08
vg1117583959 sf1117117816 11 17583959 7.03E-13 1.33E-06
vg1203668850 sf1203667849 12 3668850 1.01E-12 1.51E-06
vg0629645506 sf0629644508 6 29645506 1.33E-12 NA
vg0221761822 sf0221755953 2 21761822 2.09E-12 NA
vg0206495094 sf0206495094 2 6495094 NA 6.25E-07