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 mr1634 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
vg0223525077 sf0223519208 2 23525077 3.64E-08 3.64E-08
vg0907802333 sf0907801333 9 7802333 1.20E-07 1.20E-07
vg0808428148 sf0808427152 8 8428148 1.17E-06 1.17E-06
vg0122966094 sf0122965050 1 22966094 1.62E-06 1.62E-06
vg1117799956 sf1117333812 11 17799956 3.22E-06 3.20E-06
vg1117997623 sf1117531481 11 17997623 3.47E-06 3.48E-06