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 mr1844 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
vg0815677420 sf0815674706 8 15677420 1.70E-09 NA
vg0425010504 sf0424825365 4 25010504 9.73E-09 NA
vg1016946466 sf1016875238 10 16946466 1.88E-08 NA
vg0822237686 sf0822234973 8 22237686 2.85E-08 NA
vg0311402280 sf0311400998 3 11402280 3.69E-08 NA
vg0716086173 sf0716085180 7 16086173 6.73E-08 2.08E-06
vg0410495105 sf0410485804 4 10495105 9.94E-08 NA
vg0815985673 sf0815982959 8 15985673 1.33E-07 NA
vg0716058721 sf0716057728 7 16058721 NA 7.43E-08
vg1006612280 sf1006627903 10 6612280 NA 1.26E-06
vg0806948099 sf0806947104 8 6948099 NA 2.68E-06