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 mr1899 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
vg0139783926 sf0139782883 1 39783926 1.79E-09 NA
vg0300245476 sf0300244476 3 245476 3.00E-09 NA
vg1002941120 sf1002940097 10 2941120 7.56E-09 1.41E-06
vg0626092258 sf0626091261 6 26092258 7.69E-09 5.43E-06
vg1002941211 sf1002940188 10 2941211 1.04E-08 9.08E-07
vg1207398039 sf1207395446 12 7398039 3.07E-08 NA
vg1002940641 sf1002939618 10 2940641 1.16E-07 3.71E-06
vg0431237043 sf0431051933 4 31237043 4.86E-07 NA
vg0617087390 sf0617086393 6 17087390 1.64E-06 NA