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 mr1189 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
vg0904833561 sf0904832561 9 4833561 1.67E-08 1.35E-06
vg0224459356 sf0224453487 2 24459356 1.36E-06 3.14E-06
vg1002941120 sf1002940097 10 2941120 5.79E-06 NA
vg0917955027 sf0917954026 9 17955027 5.88E-06 NA
vg0118433922 sf0118432876 1 18433922 7.24E-06 NA
vg0620733763 sf0620732766 6 20733763 NA 1.87E-06