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 mr1311 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
vg0321576069 sf0321574579 3 21576069 8.03E-08 8.03E-08
vg0219780702 sf0219774834 2 19780702 4.90E-07 4.90E-07
vg1127480350 sf1127008737 11 27480350 8.98E-07 8.98E-07
vg0805946030 sf0805945033 8 5946030 3.29E-06 3.30E-06
vg0124420479 sf0124419435 1 24420479 4.02E-06 4.02E-06
vg0610852582 sf0610851583 6 10852582 4.84E-06 4.84E-06