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 mr1467 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
vg0724771358 sf0724770364 7 24771358 1.06E-09 NA
vg0805992743 sf0805991746 8 5992743 1.32E-09 1.11E-06
vg0902107236 sf0902106236 9 2107236 1.42E-09 2.74E-07
vg0220342715 sf0220336847 2 20342715 6.47E-09 NA
vg0904629329 sf0904628329 9 4629329 7.20E-09 4.71E-06
vg0207665511 sf0207665511 2 7665511 1.89E-08 1.67E-06
vg1117719367 sf1117253223 11 17719367 6.37E-08 4.33E-06
vg1207840077 sf1207837483 12 7840077 5.45E-07 4.27E-06