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 mr1505 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
vg0314909213 sf0314907860 3 14909213 5.02E-07 1.33E-06
vg1011666452 sf1011595267 10 11666452 6.09E-06 8.51E-06
vg0909938033 sf0909937032 9 9938033 6.12E-06 NA
vg0314891832 sf0314890479 3 14891832 6.87E-06 1.92E-06
vg1120332797 sf1119866722 11 20332797 NA 7.59E-07