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 mr1645 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
vg0527361641 sf0527298997 5 27361641 1.33E-08 NA
vg1210597588 sf1210595001 12 10597588 1.15E-07 NA
vg0516563624 sf0516506106 5 16563624 3.79E-07 3.12E-06
vg1002271573 sf1002270550 10 2271573 1.18E-06 4.47E-06
vg0223523255 sf0223517386 2 23523255 1.54E-06 1.25E-06
vg0624711737 sf0624710740 6 24711737 4.63E-06 6.17E-07