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 mr1817 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
vg0920196604 sf0920196123 9 20196604 2.83E-11 4.33E-06
vg0527488306 sf0527425662 5 27488306 1.33E-10 NA
vg0706745734 sf0706744739 7 6745734 1.36E-10 NA
vg0401680163 sf0401675712 4 1680163 1.74E-10 NA
vg0333506560 sf0333499430 3 33506560 2.25E-10 NA
vg1127668744 sf1127197131 11 27668744 3.59E-09 8.27E-07