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 mr1901 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
vg0118246218 sf0118245172 1 18246218 5.61E-09 4.11E-07
vg0117519898 sf0117518852 1 17519898 2.21E-06 NA
vg0224513696 sf0224507827 2 24513696 3.13E-06 3.68E-06
vg0300265158 sf0300264158 3 265158 3.76E-06 NA
vg1219590404 sf1219561874 12 19590404 NA 6.06E-07