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 mr1361 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
vg0313216687 sf0313215405 3 13216687 1.50E-26 NA
vg1217467868 sf1217461823 12 17467868 4.07E-26 NA
vg0815842636 sf0815839922 8 15842636 1.20E-25 NA
vg0204817972 sf0204817969 2 4817972 1.31E-25 NA
vg0125876479 sf0125875435 1 25876479 1.66E-25 NA
vg1020046067 sf1019974565 10 20046067 1.29E-24 3.89E-06
vg1020040118 sf1019968616 10 20040118 1.42E-24 2.53E-06
vg1222221962 sf1222188509 12 22221962 NA 9.06E-07
vg1210984536 sf1210981902 12 10984536 NA 1.28E-06
vg1212879871 sf1212877210 12 12879871 NA 2.05E-06
vg1214284699 sf1214282039 12 14284699 NA 2.08E-06
vg0727650948 sf0727649955 7 27650948 NA 3.25E-06
vg0314211546 sf0314210235 3 14211546 NA 3.87E-06