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 mr1646 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
vg0523663962 sf0523601383 5 23663962 3.15E-08 2.70E-06
vg0703260416 sf0703259417 7 3260416 4.48E-08 1.82E-06
vg0130351635 sf0130350591 1 30351635 4.58E-07 9.45E-07
vg1105286830 sf1105282581 11 5286830 4.97E-07 4.97E-06
vg1219631829 sf1219603299 12 19631829 1.12E-06 2.36E-06
vg1014833617 sf1014762383 10 14833617 1.17E-06 1.89E-06
vg1109529985 sf1109524562 11 9529985 2.47E-06 3.36E-06
vg0726784828 sf0726783834 7 26784828 6.96E-06 NA
vg0300249514 sf0300248514 3 249514 NA 7.57E-06