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 mr1462 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
vg0626092258 sf0626091261 6 26092258 3.03E-07 5.59E-06
vg0520065547 sf0520003023 5 20065547 2.09E-06 7.16E-06
vg1103073000 sf1103068904 11 3073000 2.40E-06 NA
vg1220172445 sf1220143887 12 20172445 2.73E-06 1.44E-06
vg1118819210 sf1118353018 11 18819210 5.06E-06 2.86E-06