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 mr1586 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
vg0911067540 sf0911066539 9 11067540 3.59E-10 1.02E-06
vg0911559557 sf0911558556 9 11559557 3.82E-10 NA
vg0113862383 sf0113861357 1 13862383 1.35E-09 NA
vg0406035761 sf0406031200 4 6035761 1.51E-09 NA
vg0406038870 sf0406034309 4 6038870 1.67E-09 3.03E-06
vg0406873204 sf0406868649 4 6873204 4.84E-09 NA
vg0911066866 sf0911065865 9 11066866 6.20E-09 2.50E-06
vg0719021807 sf0719020814 7 19021807 1.76E-07 5.62E-07
vg0808821817 sf0808820821 8 8821817 9.26E-07 NA
vg0324765360 sf0324763439 3 24765360 9.93E-07 1.24E-06
vg0325762988 sf0325761006 3 25762988 3.01E-06 4.65E-06
vg0114041371 sf0114040345 1 14041371 5.13E-06 NA
vg0824506465 sf0824503751 8 24506465 NA 1.09E-07
vg0112036174 sf0112035148 1 12036174 NA 2.95E-07
vg0618384354 sf0618383357 6 18384354 NA 9.23E-07
vg0408141966 sf0408137240 4 8141966 NA 1.67E-06