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 mr1866 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
vg0726533898 sf0726532904 7 26533898 3.35E-10 9.66E-06
vg0805958868 sf0805957871 8 5958868 7.08E-10 NA
vg0728265516 sf0728264524 7 28265516 7.59E-10 2.39E-06
vg0307075857 sf0307074855 3 7075857 8.48E-10 NA
vg0211188937 sf0211188934 2 11188937 1.04E-09 3.93E-06
vg0726739458 sf0726738464 7 26739458 6.66E-09 NA
vg0828307900 sf0828305186 8 28307900 1.07E-06 NA
vg0413685186 sf0413675900 4 13685186 2.05E-06 3.44E-06
vg0307671825 sf0307670763 3 7671825 3.41E-06 NA
vg0809707295 sf0809706299 8 9707295 NA 2.38E-06