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 mr1305 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
vg0406037789 sf0406033228 4 6037789 4.00E-10 6.38E-06
vg0406038870 sf0406034309 4 6038870 9.78E-10 1.66E-07
vg0406873204 sf0406868649 4 6873204 9.85E-10 NA
vg0911559557 sf0911558556 9 11559557 1.17E-08 NA
vg0911067540 sf0911066539 9 11067540 1.32E-08 4.22E-06
vg0334916269 sf0334909139 3 34916269 1.40E-08 NA
vg0334827698 sf0334820568 3 34827698 2.32E-08 2.53E-06
vg0719346699 sf0719345706 7 19346699 5.13E-08 NA
vg0334986236 sf0334979106 3 34986236 6.93E-08 4.70E-07
vg0226040711 sf0226034842 2 26040711 8.63E-08 6.06E-06
vg0325762988 sf0325761006 3 25762988 1.04E-06 6.27E-06
vg0111893625 sf0111892599 1 11893625 6.21E-06 4.23E-06
vg0628275391 sf0628274393 6 28275391 7.43E-06 NA
vg0824506465 sf0824503751 8 24506465 NA 2.54E-06
vg0824475026 sf0824472312 8 24475026 NA 3.33E-06