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 mr1854 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
vg1117484883 sf1117018738 11 17484883 1.81E-08 3.68E-06
vg1117473895 sf1117007750 11 17473895 2.08E-08 2.57E-06
vg0322318094 sf0322316583 3 22318094 3.64E-07 5.25E-06
vg1000599056 sf1000598032 10 599056 7.74E-06 1.40E-07
vg0201148482 sf0201148482 2 1148482 NA 4.04E-06