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 mr1460 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
vg0727914669 sf0727913676 7 27914669 8.72E-08 NA
vg0727596683 sf0727595689 7 27596683 3.10E-07 3.56E-06
Unknow sf0429164268 Unknow Unknow 9.39E-07 2.65E-06
vg0219335600 sf0219329732 2 19335600 1.17E-06 2.32E-06
vg0510163595 sf0510163524 5 10163595 1.43E-06 3.00E-06
vg0407630134 sf0407625401 4 7630134 NA 1.56E-06
vg0727958020 sf0727957027 7 27958020 NA 2.86E-06