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 mr1322 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
vg1003300042 sf1003299019 10 3300042 1.72E-13 NA
vg0818736737 sf0818734024 8 18736737 3.60E-13 NA
vg0104000380 sf0103999380 1 4000380 4.40E-13 1.41E-07
vg1021219935 sf1021148413 10 21219935 4.58E-13 NA
vg0314127667 sf0314126356 3 14127667 6.08E-13 NA
vg0314131183 sf0314129872 3 14131183 1.83E-12 NA
vg1127574082 sf1127102469 11 27574082 NA 2.87E-06