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 mr1122 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
vg0606814258 sf0606813259 6 6814258 3.15E-11 NA
vg0610731331 sf0610730332 6 10731331 6.24E-10 NA
vg1127029126 sf1126557513 11 27029126 1.08E-09 NA
vg0617611502 sf0617610505 6 17611502 2.61E-09 NA
vg1122446629 sf1121980500 11 22446629 1.16E-08 NA
vg1122447657 sf1121981528 11 22447657 9.10E-08 5.61E-06
vg0114234917 sf0114233891 1 14234917 1.70E-06 2.47E-06
vg0506624382 sf0506624323 5 6624382 2.88E-06 NA
vg0820541103 sf0820538390 8 20541103 5.54E-06 2.75E-06