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 mr1806 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
vg0139928356 sf0139927313 1 39928356 1.31E-16 1.60E-06
vg0620807166 sf0620806169 6 20807166 1.16E-14 6.75E-06
vg0904007553 sf0904006553 9 4007553 6.16E-14 NA
vg0620801911 sf0620800914 6 20801911 8.11E-14 2.51E-07
vg0232479992 sf0232474123 2 32479992 8.66E-14 NA
vg0724527790 sf0724526796 7 24527790 8.73E-14 NA
vg0142487665 sf0142486621 1 42487665 6.75E-12 3.39E-06
vg1111945410 sf1111939727 11 11945410 1.08E-11 NA
vg0804311745 sf0804310748 8 4311745 1.52E-10 6.24E-07
vg0716888581 sf0716887588 7 16888581 4.16E-10 3.81E-07
vg0103132043 sf0103131043 1 3132043 NA 4.14E-08
vg0804590579 sf0804589582 8 4590579 NA 1.33E-07
vg0102688112 sf0102687112 1 2688112 NA 2.53E-07
vg0804261000 sf0804260003 8 4261000 NA 2.24E-06
vg0607961607 sf0607960608 6 7961607 NA 2.66E-06
vg0517577873 sf0517517516 5 17577873 NA 2.79E-06
vg0804308292 sf0804307295 8 4308292 NA 3.03E-06
vg0805159916 sf0805158919 8 5159916 NA 3.22E-06
vg0528383107 sf0528320462 5 28383107 NA 3.28E-06
vg0321930073 sf0321928582 3 21930073 NA 3.79E-06
vg0501151102 sf0501151086 5 1151102 NA 4.53E-06
vg0316269069 sf0316267716 3 16269069 NA 4.85E-06