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 mr1050 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
vg0330824541 sf0330817428 3 30824541 2.25E-16 6.88E-07
vg0330783477 sf0330776364 3 30783477 1.10E-13 1.89E-07
vg1217046946 sf1217040900 12 17046946 1.92E-13 NA
vg1104581382 sf1104577284 11 4581382 4.46E-13 NA
vg0424050531 sf0423865392 4 24050531 1.34E-12 NA
vg0507313026 sf0507312968 5 7313026 1.90E-12 NA
vg0827225389 sf0827222675 8 27225389 7.89E-12 NA
vg1215059534 sf1215056876 12 15059534 NA 4.63E-07
vg0604730580 sf0604729581 6 4730580 NA 2.77E-06