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 mr1140 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
vg0406519287 sf0406514730 4 6519287 1.18E-23 4.47E-17
vg0406464503 sf0406459946 4 6464503 1.09E-22 1.04E-15
vg1016565386 sf1016494159 10 16565386 2.73E-11 3.02E-06
vg1122614316 sf1122148187 11 22614316 3.30E-09 NA
vg0823019901 sf0823017188 8 23019901 2.19E-08 2.41E-06
vg0722546543 sf0722545550 7 22546543 3.37E-08 NA
vg0722626782 sf0722625789 7 22626782 9.39E-08 2.24E-06