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 mr1730 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
vg0726726898 sf0726725904 7 26726898 8.13E-11 8.43E-06
vg0413685186 sf0413675900 4 13685186 1.74E-10 2.63E-09
vg0313425592 sf0313424310 3 13425592 5.59E-09 NA
vg0307075857 sf0307074855 3 7075857 5.93E-09 NA
vg1214863744 sf1214861085 12 14863744 7.57E-09 NA
vg0728265516 sf0728264524 7 28265516 1.07E-08 4.16E-06
vg0125628571 sf0125627527 1 25628571 3.64E-06 NA
vg0828307900 sf0828305186 8 28307900 4.10E-06 NA