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 mr1596 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
vg0902343614 sf0902342614 9 2343614 1.13E-09 1.39E-07
vg0901762072 sf0901761072 9 1762072 1.59E-09 1.71E-07
vg0900708420 sf0900707420 9 708420 2.37E-09 7.54E-06
vg1203113723 sf1203112726 12 3113723 5.55E-09 6.09E-06
vg0432306627 sf0432121519 4 32306627 1.67E-08 4.53E-06
vg0905970596 sf0905969596 9 5970596 1.76E-08 5.55E-06
vg0410044585 sf0410035282 4 10044585 6.19E-08 4.81E-06
vg0401697946 sf0401693495 4 1697946 9.74E-08 2.39E-06
vg0423636908 sf0423451765 4 23636908 1.12E-07 2.39E-06
vg0904278800 sf0904277800 9 4278800 1.17E-07 3.08E-06
vg0432280842 sf0432095735 4 32280842 3.88E-07 2.01E-06
vg0223074046 sf0223068177 2 23074046 4.03E-07 3.03E-07
vg0916030541 sf0916029540 9 16030541 3.24E-06 9.25E-07