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 mr1569 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
vg1203022431 sf1203021433 12 3022431 1.77E-08 NA
vg0323063280 sf0323061768 3 23063280 5.21E-08 NA
vg0827768147 sf0827765433 8 27768147 9.41E-08 NA
vg1125735290 sf1125269129 11 25735290 3.65E-07 5.04E-06
vg0405053182 sf0405048621 4 5053182 1.89E-06 NA
vg0335708563 sf0335701432 3 35708563 4.19E-06 NA
vg1127979337 sf1127507723 11 27979337 5.81E-06 6.73E-07