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 mr1931 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
vg0329226011 sf0329219063 3 29226011 9.52E-09 NA
vg0218969543 sf0218963674 2 18969543 1.41E-08 NA
vg1117074550 sf1116608402 11 17074550 8.12E-08 NA
vg1225594396 sf1225560791 12 25594396 3.08E-07 NA
vg0217924433 sf0217918564 2 17924433 6.47E-07 4.10E-06
vg1108800737 sf1108795347 11 8800737 5.29E-06 1.22E-06
vg0315668204 sf0315666851 3 15668204 8.19E-06 3.63E-06