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 mr1891 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
vg0217658679 sf0217652809 2 17658679 1.65E-35 NA
vg0211327076 sf0211327073 2 11327076 1.75E-35 2.10E-06
vg1014788162 sf1014716928 10 14788162 7.05E-35 NA
vg0716997079 sf0716996086 7 16997079 4.54E-34 NA
vg0907293804 sf0907292804 9 7293804 7.59E-34 NA
vg0717129729 sf0717128736 7 17129729 1.11E-33 NA
vg0907175535 sf0907174535 9 7175535 4.76E-32 2.34E-08
vg0232755756 sf0232749887 2 32755756 2.40E-31 4.05E-07
vg0420103716 sf0419931753 4 20103716 NA 4.49E-06
vg0710985476 sf0710984482 7 10985476 NA 6.12E-06