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 mr1767 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
vg0205287313 sf0205287311 2 5287313 1.00E-26 5.03E-09
vg0205285714 sf0205285712 2 5285714 3.62E-26 2.69E-09
vg0138531742 sf0138530699 1 38531742 3.77E-20 NA
vg1105668680 sf1105664432 11 5668680 6.97E-19 NA
vg0221210286 sf0221204418 2 21210286 1.26E-18 NA
vg1207875018 sf1207872424 12 7875018 1.52E-18 NA
vg1214656787 sf1214654127 12 14656787 5.94E-17 5.48E-08
vg0205035629 sf0205035626 2 5035629 1.12E-15 4.30E-06
vg0518984986 sf0518922470 5 18984986 NA 1.35E-06
vg0805992743 sf0805991746 8 5992743 NA 2.94E-06