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 mr1638 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
vg1104228562 sf1104224464 11 4228562 1.21E-19 2.83E-16
vg1104131901 sf1104127803 11 4131901 3.24E-19 2.37E-16
vg1104456316 sf1104452218 11 4456316 1.85E-09 4.07E-07
vg1104435123 sf1104431025 11 4435123 1.36E-08 4.82E-06
vg0411097811 sf0411088512 4 11097811 2.34E-06 3.26E-06
vg1103472398 sf1103468301 11 3472398 5.84E-06 4.59E-06