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 mr1994 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
vg0135548077 sf0135547034 1 35548077 1.21E-09 NA
vg0133032292 sf0133031248 1 33032292 1.41E-08 NA
vg0809186402 sf0809185406 8 9186402 1.65E-08 NA
vg1004077056 sf1004076032 10 4077056 8.05E-08 NA
vg0906299067 sf0906298067 9 6299067 1.46E-06 1.08E-06
vg0805869798 sf0805868801 8 5869798 3.12E-06 3.16E-06