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 mr1107 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
vg0719039736 sf0719038743 7 19039736 8.19E-12 8.51E-14
vg0719053396 sf0719052403 7 19053396 1.23E-11 6.67E-11
vg0719040385 sf0719039392 7 19040385 1.87E-11 1.26E-13
vg0432050351 sf0431865243 4 32050351 5.10E-08 8.27E-06
vg0816273372 sf0816270658 8 16273372 7.53E-08 NA
vg1015917537 sf1015846307 10 15917537 1.31E-07 1.60E-06