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 mr1008 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
vg0133408824 sf0133407780 1 33408824 1.23E-12 7.52E-12
vg0133636638 sf0133635594 1 33636638 1.74E-11 2.30E-12
vg0133697207 sf0133696163 1 33697207 9.33E-11 1.16E-11
vg0521856508 sf0521793950 5 21856508 6.85E-08 1.58E-06
vg0133425658 sf0133424614 1 33425658 1.10E-07 1.36E-07
vg0229931163 sf0229925294 2 29931163 5.70E-07 4.28E-06
vg0106778059 sf0106777059 1 6778059 7.77E-07 8.72E-07
vg0921567751 sf0921567270 9 21567751 NA 2.85E-06