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 mr1181 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
vg0724528315 sf0724527321 7 24528315 5.18E-10 4.36E-07
vg0724427457 sf0724426463 7 24427457 1.51E-08 3.80E-07
vg1217540080 sf1217534035 12 17540080 2.50E-08 NA
vg0724517813 sf0724516819 7 24517813 2.97E-08 2.00E-06
vg0914025711 sf0914024710 9 14025711 3.37E-08 NA
vg1123837414 sf1123371284 11 23837414 3.88E-08 NA
vg0427788963 sf0427603823 4 27788963 4.20E-08 NA
vg0501188064 sf0501188048 5 1188064 3.93E-07 NA
vg0608663055 sf0608662056 6 8663055 2.58E-06 NA