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 mr1579 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
vg1124903385 sf1124437225 11 24903385 1.83E-07 1.83E-07
vg1124810339 sf1124344179 11 24810339 3.62E-07 3.62E-07
vg1122062760 sf1121596631 11 22062760 5.57E-07 5.58E-07
vg1122960079 sf1122493950 11 22960079 1.82E-06 1.82E-06
vg0824864741 sf0824862027 8 24864741 2.74E-06 2.74E-06
vg0123762848 sf0123761804 1 23762848 3.29E-06 3.29E-06