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 mr1280 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
vg0303534207 sf0303533203 3 3534207 2.18E-10 NA
vg0414209075 sf0414199791 4 14209075 8.03E-10 5.23E-06
vg0303605279 sf0303604275 3 3605279 2.77E-09 NA
vg0419787605 sf0419615642 4 19787605 3.82E-09 NA
vg1210431367 sf1210428780 12 10431367 4.34E-09 NA
vg0525484560 sf0525421981 5 25484560 5.43E-09 NA
vg1003719342 sf1003718319 10 3719342 3.97E-06 5.52E-07