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 mr1162 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
vg1216678067 sf1216672021 12 16678067 1.18E-08 1.18E-08
vg0525542114 sf0525479535 5 25542114 1.10E-06 1.10E-06
vg0916231494 sf0916230493 9 16231494 3.34E-06 3.34E-06
vg1010276752 sf1010205573 10 10276752 3.73E-06 3.73E-06
vg1208455296 sf1208452703 12 8455296 4.00E-06 4.00E-06