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 mr1565 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
vg0433924853 sf0433739750 4 33924853 1.97E-09 1.25E-08
vg0200274146 sf0200274146 2 274146 3.24E-09 8.36E-08
vg0121172559 sf0121171514 1 21172559 5.16E-09 7.39E-08
vg1000393294 sf1000392294 10 393294 5.88E-08 NA
vg0401598934 sf0401594483 4 1598934 3.89E-07 3.56E-06