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 mr1862 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
vg1018998107 sf1018926664 10 18998107 3.74E-50 1.69E-07
vg1019088726 sf1019017283 10 19088726 6.76E-50 2.43E-09
vg1224594467 sf1224560921 12 24594467 3.00E-45 NA
vg0216763637 sf0216757767 2 16763637 1.03E-43 NA
vg0433820620 sf0433635511 4 33820620 1.20E-43 NA
vg0106176553 sf0106175553 1 6176553 3.40E-43 NA
vg0523098113 sf0523035554 5 23098113 2.18E-39 NA
vg1018822915 sf1018751471 10 18822915 NA 2.54E-07
vg0106187082 sf0106186082 1 6187082 NA 3.09E-06
vg0402290555 sf0402286150 4 2290555 NA 3.99E-06
vg0815289622 sf0815286908 8 15289622 NA 4.00E-06