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 mr1077 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
vg0222741535 sf0222735666 2 22741535 2.76E-59 1.82E-27
vg0222719698 sf0222713829 2 22719698 4.36E-58 1.09E-27
vg0600835519 sf0600834520 6 835519 2.14E-31 NA
vg0626852375 sf0626851378 6 26852375 1.96E-28 NA
vg0716110434 sf0716109441 7 16110434 3.00E-28 NA
vg0604641288 sf0604640289 6 4641288 3.15E-27 NA
vg0222725003 sf0222719134 2 22725003 NA 2.27E-09
vg0224382271 sf0224376402 2 24382271 NA 6.89E-07
vg0223755105 sf0223749236 2 23755105 NA 7.40E-07
vg0610548373 sf0610547374 6 10548373 NA 1.98E-06
vg0704640725 sf0704639726 7 4640725 NA 2.97E-06
vg0222807259 sf0222801390 2 22807259 NA 3.22E-06