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 mr1782 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
vg0229433488 sf0229427619 2 29433488 2.31E-14 NA
vg0920162336 sf0920161855 9 20162336 1.45E-13 NA
vg0235871188 sf0235865319 2 35871188 2.09E-13 NA
vg0125680354 sf0125679310 1 25680354 7.68E-13 NA
vg0609394624 sf0609393625 6 9394624 7.95E-13 NA
vg0118775740 sf0118774695 1 18775740 NA 4.08E-07