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 mr1645 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
vg0321576069 sf0321574579 3 21576069 8.72E-08 8.73E-08
vg0222337580 sf0222331711 2 22337580 1.27E-07 1.27E-07
vg0416930919 sf0416758961 4 16930919 8.82E-07 8.82E-07
vg0227713751 sf0227707882 2 27713751 1.80E-06 1.81E-06
vg1010927325 sf1010856145 10 10927325 3.91E-06 3.91E-06
vg0605572207 sf0605571208 6 5572207 4.33E-06 4.33E-06