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 mr1401 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
vg0903736728 sf0903735728 9 3736728 8.80E-07 4.24E-06
vg0208155990 sf0208155989 2 8155990 1.47E-06 1.90E-07
vg0810948653 sf0810947658 8 10948653 1.94E-06 1.89E-06
vg0811281856 sf0811280861 8 11281856 2.12E-06 3.63E-06
vg0307860069 sf0307859007 3 7860069 4.50E-06 1.77E-06
vg0726584856 sf0726583862 7 26584856 5.69E-06 NA
vg0612068302 sf0612067303 6 12068302 7.54E-06 3.62E-06