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 mr1669 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
vg1122515087 sf1122048958 11 22515087 1.82E-12 NA
vg0122697025 sf0122695980 1 22697025 2.86E-12 NA
vg1013289010 sf1013217779 10 13289010 1.68E-10 NA
vg0615582626 sf0615581628 6 15582626 2.14E-10 NA
vg0315348932 sf0315347579 3 15348932 2.73E-10 NA
vg0515523564 sf0515466105 5 15523564 1.39E-09 NA
vg1117514629 sf1117048484 11 17514629 5.12E-09 NA
vg0102459995 sf0102458995 1 2459995 NA 1.05E-06
vg0412456522 sf0412447237 4 12456522 NA 3.35E-06