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 mr1582 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
vg0203129511 sf0203129509 2 3129511 3.46E-12 NA
vg0100936862 sf0100935862 1 936862 1.01E-11 NA
vg0141812887 sf0141811844 1 41812887 1.61E-11 NA
vg0616543691 sf0616542693 6 16543691 1.61E-11 NA
vg1217535382 sf1217529337 12 17535382 1.79E-11 NA
vg0101207412 sf0101206412 1 1207412 5.27E-11 NA
vg1207398363 sf1207395770 12 7398363 2.03E-08 NA
vg1116856270 sf1116391149 11 16856270 2.45E-07 8.60E-07
vg0622673369 sf0622672372 6 22673369 NA 1.52E-06
vg0719624629 sf0719623636 7 19624629 NA 1.60E-06
vg0224471358 sf0224465489 2 24471358 NA 2.95E-06