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 mr1057 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
vg0208607058 sf0208607057 2 8607058 3.66E-07 2.67E-06
vg0222272774 sf0222266905 2 22272774 4.49E-07 1.88E-07
vg0221717035 sf0221711166 2 21717035 4.89E-07 1.04E-07
vg0423542197 sf0423357054 4 23542197 9.58E-07 NA
vg0217864370 sf0217858501 2 17864370 1.04E-06 4.42E-07
vg0407832314 sf0407827582 4 7832314 1.37E-06 9.56E-07
vg0501597771 sf0501597755 5 1597771 1.49E-06 2.60E-06
vg0310223480 sf0310222396 3 10223480 1.72E-06 9.25E-07
vg1104535450 sf1104531352 11 4535450 3.14E-06 1.36E-06
vg0217797694 sf0217791825 2 17797694 9.68E-06 1.14E-06
vg1213797975 sf1213795313 12 13797975 9.72E-06 2.18E-06