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 mr1920 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
vg0604287833 sf0604286834 6 4287833 5.53E-11 3.88E-09
vg0603908292 sf0603907293 6 3908292 5.57E-08 NA
vg0908546508 sf0908545507 9 8546508 8.53E-08 NA
vg0826159919 sf0826157205 8 26159919 1.48E-07 1.50E-07
vg0310227268 sf0310226184 3 10227268 2.33E-06 NA
vg1202614240 sf1202613242 12 2614240 2.91E-06 8.86E-07
vg0129921548 sf0129920503 1 29921548 NA 8.35E-06