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 mr1941 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
vg0518016012 sf0517955498 5 18016012 3.90E-09 7.66E-07
vg0700086162 sf0700085162 7 86162 1.10E-08 NA
vg0515035963 sf0514978505 5 15035963 1.59E-08 1.94E-06
vg0329021808 sf0329014860 3 29021808 3.93E-08 NA
vg0216351003 sf0216345133 2 16351003 3.50E-06 NA