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 mr1633 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 3.35E-15 4.45E-12
vg0205295837 sf0205295835 2 5295837 3.53E-15 3.97E-12
vg0131940401 sf0131939357 1 31940401 5.39E-09 8.11E-07
vg1104316746 sf1104312648 11 4316746 4.61E-08 7.64E-07
vg1119033238 sf1118566926 11 19033238 2.96E-06 NA