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 mr1297 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
vg0615411425 sf0615410426 6 15411425 3.02E-07 3.94E-07
vg0826159860 sf0826157146 8 26159860 6.10E-07 3.51E-06
vg0212359529 sf0212359525 2 12359529 2.79E-06 3.18E-06
vg0519573025 sf0519510509 5 19573025 4.88E-06 NA
vg0329917563 sf0329910602 3 29917563 NA 1.22E-06