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 mr1641 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
vg0205284721 sf0205284719 2 5284721 2.29E-26 1.25E-10
vg0132983504 sf0132982460 1 32983504 1.97E-17 NA
vg0910822833 sf0910821832 9 10822833 2.50E-17 NA
vg0129865528 sf0129864483 1 29865528 5.22E-17 NA
vg0302287012 sf0302286008 3 2287012 9.28E-17 4.67E-06
vg1119463807 sf1118997495 11 19463807 6.91E-16 4.38E-07
vg0200741581 sf0200741581 2 741581 4.49E-15 2.32E-06
vg1016837158 sf1016765930 10 16837158 2.42E-14 1.50E-06
vg0917042786 sf0917041785 9 17042786 1.07E-13 3.61E-07
vg0332544561 sf0332537434 3 32544561 NA 2.61E-06
vg1016899401 sf1016828173 10 16899401 NA 3.60E-06