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 mr1822 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
vg0607659813 sf0607658814 6 7659813 1.38E-07 1.39E-07
vg0808427097 sf0808426101 8 8427097 3.91E-07 3.91E-07
vg0421454162 sf0421282213 4 21454162 4.26E-07 4.27E-07
vg0904149706 sf0904148706 9 4149706 8.20E-07 8.21E-07
vg0726559146 sf0726558152 7 26559146 1.08E-06 1.08E-06
vg0629093290 sf0629092292 6 29093290 1.14E-06 1.14E-06
vg1121957619 sf1121491490 11 21957619 1.40E-06 1.40E-06
vg0420718113 sf0420546156 4 20718113 1.90E-06 1.91E-06
vg0404762368 sf0404757807 4 4762368 3.07E-06 3.06E-06