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 mr1212 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
vg0719246584 sf0719245591 7 19246584 5.82E-11 1.50E-07
vg0719208431 sf0719207438 7 19208431 1.61E-10 1.00E-07
vg0719208783 sf0719207790 7 19208783 2.22E-10 1.00E-07
vg1124078519 sf1123612389 11 24078519 2.94E-06 NA
vg0216716710 sf0216710840 2 16716710 5.47E-06 1.23E-06
vg0528175027 sf0528112382 5 28175027 NA 4.56E-06