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 mr1208 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
vg0129148600 sf0129147555 1 29148600 4.36E-36 NA
vg0328464269 sf0328457322 3 28464269 3.59E-35 NA
vg0229321816 sf0229315947 2 29321816 5.46E-35 NA
vg1204602031 sf1204601019 12 4602031 6.47E-35 NA
vg0520366263 sf0520303736 5 20366263 8.97E-35 NA
vg0520337395 sf0520274868 5 20337395 1.39E-33 9.57E-06
vg0904650982 sf0904649982 9 4650982 6.22E-32 3.07E-06
vg0922057692 sf0922057211 9 22057692 7.85E-31 1.02E-11
vg0626387314 sf0626386317 6 26387314 NA 1.30E-07
vg1019669777 sf1019598278 10 19669777 NA 3.63E-07
vg0901852241 sf0901851241 9 1852241 NA 3.90E-07
vg1200639944 sf1200638944 12 639944 NA 1.63E-06
vg0900606355 sf0900605355 9 606355 NA 4.12E-06