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 mr1795 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
vg0406395970 sf0406391410 4 6395970 4.16E-59 3.04E-06
vg0522551271 sf0522488713 5 22551271 5.38E-59 NA
vg0406421004 sf0406416444 4 6421004 9.46E-59 1.29E-06
vg0314275748 sf0314274437 3 14275748 3.68E-58 NA
vg0211839911 sf0211839907 2 11839911 4.41E-58 5.63E-06
vg0612943979 sf0612942980 6 12943979 5.39E-58 NA
vg0235439519 sf0235433650 2 35439519 5.37E-56 NA
vg0222742146 sf0222736277 2 22742146 NA 5.18E-14
vg1112909023 sf1112445344 11 12909023 NA 3.29E-08
vg0224620629 sf0224614760 2 24620629 NA 4.23E-08
vg0406526884 sf0406522327 4 6526884 NA 1.40E-07
vg0222598995 sf0222593126 2 22598995 NA 1.72E-07
vg0217679973 sf0217674103 2 17679973 NA 1.10E-06
vg0224574434 sf0224568565 2 24574434 NA 1.60E-06
vg0111184479 sf0111183455 1 11184479 NA 2.69E-06
vg0124115850 sf0124114806 1 24115850 NA 3.05E-06
vg0105373556 sf0105372556 1 5373556 NA 3.08E-06
vg0606129619 sf0606128620 6 6129619 NA 3.40E-06
vg0224660997 sf0224655128 2 24660997 NA 4.38E-06