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 mr1171 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
vg0516508609 sf0516451091 5 16508609 3.75E-09 3.75E-09
vg0516381476 sf0516323958 5 16381476 2.09E-08 2.09E-08
vg0800888732 sf0800887734 8 888732 1.37E-06 1.37E-06
vg0816670160 sf0816667446 8 16670160 4.03E-06 4.03E-06
vg0224434814 sf0224428945 2 24434814 4.12E-06 4.12E-06
vg1121614615 sf1121148492 11 21614615 4.73E-06 4.73E-06
vg0810920351 sf0810919356 8 10920351 5.97E-06 5.97E-06