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 mr1556 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
vg0332903796 sf0332896666 3 32903796 4.37E-10 NA
vg0233881588 sf0233875719 2 33881588 1.25E-09 NA
vg1106481643 sf1106477395 11 6481643 2.31E-09 NA
vg0313174041 sf0313172759 3 13174041 3.18E-09 NA
vg0608257591 sf0608256592 6 8257591 3.21E-09 NA
vg0315356877 sf0315355524 3 15356877 7.19E-09 NA
vg0623156256 sf0623155259 6 23156256 4.98E-08 6.00E-07