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 mr1388 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
vg0323555815 sf0323553989 3 23555815 2.14E-08 1.94E-06
vg0719048035 sf0719047042 7 19048035 4.97E-08 5.56E-06
vg1217449731 sf1217443686 12 17449731 6.21E-08 5.25E-06
vg1108092829 sf1108088574 11 8092829 2.92E-07 1.29E-06
vg0142428882 sf0142427838 1 42428882 6.32E-07 2.91E-06