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 mr1379 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
vg0216625467 sf0216619597 2 16625467 3.90E-18 5.52E-08
vg0216595921 sf0216590051 2 16595921 3.33E-16 9.31E-07
vg0709509554 sf0709508560 7 9509554 3.16E-14 NA
vg0219876906 sf0219871038 2 19876906 1.52E-13 4.99E-06
vg0716257753 sf0716256760 7 16257753 5.97E-13 NA
vg0220864582 sf0220858714 2 20864582 1.07E-12 NA
vg0414510569 sf0414501283 4 14510569 2.21E-12 2.47E-07
vg0221138308 sf0221132440 2 21138308 1.06E-11 3.58E-06
vg0406358263 sf0406353703 4 6358263 1.10E-11 3.12E-06
vg0216691537 sf0216685667 2 16691537 3.87E-11 1.01E-08
vg0406154461 sf0406149901 4 6154461 9.30E-10 NA
vg0327447631 sf0327440684 3 27447631 1.14E-09 1.05E-07
vg1009327648 sf1009256469 10 9327648 NA 5.63E-08
vg0315369570 sf0315368217 3 15369570 NA 5.44E-07
vg0327391604 sf0327384657 3 27391604 NA 1.10E-06
vg1009535675 sf1009464496 10 9535675 NA 1.65E-06
vg0314967098 sf0314965745 3 14967098 NA 2.07E-06
vg0701261601 sf0701260601 7 1261601 NA 2.53E-06
vg0109366509 sf0109365485 1 9366509 NA 2.55E-06
vg0216864568 sf0216858698 2 16864568 NA 2.76E-06
vg0702108979 sf0702107980 7 2108979 NA 3.23E-06
vg0324795678 sf0324793757 3 24795678 NA 3.26E-06
vg0216461958 sf0216456088 2 16461958 NA 4.03E-06
vg0301312981 sf0301311979 3 1312981 NA 7.56E-06