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 mr1770 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
vg0302293724 sf0302292720 3 2293724 1.12E-08 1.12E-08
vg0104342395 sf0104341395 1 4342395 4.38E-07 4.38E-07
vg0910238584 sf0910237583 9 10238584 1.36E-06 1.36E-06
vg0134937509 sf0134936466 1 34937509 1.60E-06 1.60E-06
vg0504904086 sf0504904064 5 4904086 2.25E-06 2.25E-06
vg0417576751 sf0417404793 4 17576751 3.77E-06 3.77E-06
vg0816930005 sf0816927291 8 16930005 4.00E-06 4.00E-06