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 mr1282 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
vg0803654150 sf0803653153 8 3654150 1.45E-16 5.98E-10
vg0401895360 sf0401890956 4 1895360 2.20E-15 1.45E-07
vg0724248089 sf0724247095 7 24248089 4.43E-15 2.94E-06
vg0401900537 sf0401896133 4 1900537 8.32E-15 9.44E-08
vg0411655204 sf0411645910 4 11655204 2.39E-14 1.83E-06
vg0917104880 sf0917103879 9 17104880 3.18E-14 NA
vg0412751761 sf0412742471 4 12751761 3.51E-14 3.30E-07
vg0134272325 sf0134271282 1 34272325 8.18E-14 1.78E-08
vg0618798718 sf0618797721 6 18798718 1.55E-13 3.64E-07
vg0409634255 sf0409624953 4 9634255 2.10E-13 4.63E-06
vg0137195833 sf0137194790 1 37195833 4.00E-13 8.33E-07
vg0410865996 sf0410856697 4 10865996 9.70E-13 NA
vg0618517700 sf0618516703 6 18517700 2.03E-11 3.82E-07
vg0803657241 sf0803656244 8 3657241 NA 8.42E-10
vg0917466490 sf0917465489 9 17466490 NA 1.88E-06
vg1105347465 sf1105343216 11 5347465 NA 2.63E-06
vg0709781857 sf0709780863 7 9781857 NA 3.07E-06
vg0106645732 sf0106644732 1 6645732 NA 3.73E-06
vg0621761253 sf0621760256 6 21761253 NA 3.88E-06