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 mr1926 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
vg1000757961 sf1000756937 10 757961 1.32E-25 3.19E-16
vg0528039299 sf0527976654 5 28039299 6.53E-13 6.43E-07
vg0528146502 sf0528083857 5 28146502 8.19E-13 2.12E-07
vg1010974418 sf1010903238 10 10974418 1.70E-11 9.99E-06
vg0700359527 sf0700358527 7 359527 1.79E-11 2.29E-06
vg1128842480 sf1128319259 11 28842480 4.25E-11 2.75E-06
vg1128791777 sf1128268556 11 28791777 1.02E-10 1.28E-06
vg1119999188 sf1119533111 11 19999188 2.94E-09 5.10E-07
vg0328403714 sf0328396767 3 28403714 1.73E-08 4.15E-07
vg1125047295 sf1124581135 11 25047295 4.72E-08 3.41E-07
vg1125090609 sf1124624449 11 25090609 NA 3.55E-11
vg1125117714 sf1124651554 11 25117714 NA 5.21E-10
vg1004777607 sf1004794144 10 4777607 NA 3.53E-07
vg1000740409 sf1000739385 10 740409 NA 3.91E-07
vg0328105679 sf0328098733 3 28105679 NA 1.65E-06
vg1004766552 sf1004783089 10 4766552 NA 3.38E-06
vg0706566801 sf0706565806 7 6566801 NA 4.00E-06
vg0827595612 sf0827592898 8 27595612 NA 4.87E-06