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 mr1045 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
vg0207217318 sf0207217318 2 7217318 4.78E-10 NA
vg0315006256 sf0315004903 3 15006256 7.91E-10 2.81E-06
vg0414221572 sf0414212285 4 14221572 3.31E-09 NA
vg0314728343 sf0314727030 3 14728343 7.82E-09 1.21E-06
vg0812695428 sf0812693253 8 12695428 9.25E-09 NA
vg0809871494 sf0809870498 8 9871494 1.26E-08 NA
vg1105816397 sf1105812149 11 5816397 5.64E-07 4.13E-06
vg0231268830 sf0231262961 2 31268830 1.13E-06 2.04E-06
vg0720705444 sf0720704451 7 20705444 2.42E-06 NA
vg1014864085 sf1014792851 10 14864085 4.33E-06 NA
vg0208546299 sf0208546298 2 8546299 NA 4.46E-06