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 mr1641 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
vg0805098079 sf0805097082 8 5098079 8.89E-08 8.89E-08
vg0223170147 sf0223164278 2 23170147 7.06E-07 7.06E-07
vg0805963026 sf0805962029 8 5963026 1.01E-06 1.01E-06
vg1209889554 sf1209886964 12 9889554 1.25E-06 1.25E-06
vg0607961607 sf0607960608 6 7961607 3.80E-06 3.80E-06
vg0405742124 sf0405737563 4 5742124 4.40E-06 4.40E-06