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 mr1334 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
vg1220404630 sf1220376072 12 20404630 8.83E-39 7.25E-22
vg1220795056 sf1220761604 12 20795056 1.20E-38 2.81E-24
vg1220360743 sf1220332185 12 20360743 6.97E-24 5.95E-12
vg1224806805 sf1224773259 12 24806805 6.44E-20 1.43E-07
vg0216569039 sf0216563169 2 16569039 2.88E-19 1.54E-07
vg1216132362 sf1216129658 12 16132362 2.87E-18 NA
vg1019887815 sf1019816315 10 19887815 1.39E-16 NA
vg0223104206 sf0223098337 2 23104206 NA 1.11E-07
vg1220222656 sf1220194098 12 20222656 NA 2.21E-07
vg1220221344 sf1220192786 12 20221344 NA 3.24E-07