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 mr1593 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
vg0507128411 sf0507128353 5 7128411 1.69E-129 1.10E-66
vg0507169486 sf0507169428 5 7169486 5.44E-107 2.52E-59
vg0507141002 sf0507140944 5 7141002 6.11E-39 2.06E-37
vg0507206367 sf0507206309 5 7206367 1.06E-38 2.78E-44
vg0507350915 sf0507350857 5 7350915 1.05E-28 1.49E-09
vg0506900331 sf0506900273 5 6900331 8.49E-25 NA
vg0511832236 sf0511832166 5 11832236 1.75E-21 NA
vg0507287653 sf0507287595 5 7287653 2.46E-21 8.61E-11
vg0506795354 sf0506795296 5 6795354 2.08E-15 9.46E-07
vg0519750092 sf0519687576 5 19750092 5.32E-15 4.91E-06
vg0507074482 sf0507074424 5 7074482 5.70E-15 4.02E-20
vg0507088437 sf0507088379 5 7088437 1.44E-13 4.46E-13
vg0507207626 sf0507207568 5 7207626 NA 3.32E-10
vg0506751886 sf0506751828 5 6751886 NA 1.15E-08
vg0506970223 sf0506970165 5 6970223 NA 7.60E-08
vg0510456115 sf0510459274 5 10456115 NA 9.31E-08
vg0508296043 sf0508295983 5 8296043 NA 4.99E-07
vg0137371529 sf0137370486 1 37371529 NA 1.51E-06
vg0314939063 sf0314937710 3 14939063 NA 1.78E-06
vg0512828870 sf0512771792 5 12828870 NA 1.89E-06
vg0107990856 sf0107989856 1 7990856 NA 2.46E-06
vg0121586179 sf0121585134 1 21586179 NA 2.84E-06
vg0513378621 sf0513321169 5 13378621 NA 2.85E-06
vg0506970510 sf0506970452 5 6970510 NA 3.55E-06
vg0128647202 sf0128646157 1 28647202 NA 3.56E-06
vg0517271938 sf0517211581 5 17271938 NA 4.39E-06
vg0507108976 sf0507108918 5 7108976 NA 4.43E-06