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 mr1399 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
vg0601350335 sf0601349336 6 1350335 6.03E-13 NA
vg0607606976 sf0607605977 6 7606976 1.60E-12 NA
vg0607629449 sf0607628450 6 7629449 2.18E-12 NA
vg0718376392 sf0718375399 7 18376392 2.51E-11 NA
vg0919933719 sf0919933238 9 19933719 5.11E-11 NA
vg0200832081 sf0200832081 2 832081 5.74E-11 NA
vg0725044370 sf0725043376 7 25044370 7.35E-09 4.85E-06
vg0808640641 sf0808639645 8 8640641 NA 1.46E-06
vg0405980260 sf0405975700 4 5980260 NA 4.89E-06