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 mr1288 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
vg1122514350 sf1122048221 11 22514350 9.41E-09 2.62E-07
vg0703631746 sf0703630747 7 3631746 2.79E-07 1.84E-06
vg1125763864 sf1125297703 11 25763864 5.58E-07 4.85E-06
vg1016847285 sf1016776057 10 16847285 NA 6.34E-07
vg1215235888 sf1218062462 12 15235888 NA 7.74E-07
vg1023170552 sf1023099024 10 23170552 NA 2.34E-06
vg0304945886 sf0304944888 3 4945886 NA 3.64E-06