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 mr1909 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
vg0205285714 sf0205285712 2 5285714 5.22E-19 6.02E-10
vg0205287313 sf0205287311 2 5287313 9.42E-19 6.98E-11
vg1214638617 sf1214635957 12 14638617 2.18E-12 1.18E-06
vg1214656787 sf1214654127 12 14656787 5.13E-12 9.12E-08
vg1207510896 sf1207508302 12 7510896 1.75E-10 NA
vg0138531742 sf0138530699 1 38531742 1.84E-10 NA
vg1105668552 sf1105664304 11 5668552 1.94E-10 NA
vg0808100775 sf0808099779 8 8100775 6.42E-10 3.31E-06
vg1219590404 sf1219561874 12 19590404 6.88E-10 3.21E-07
vg0130364087 sf0130363043 1 30364087 1.54E-07 NA
vg0400667852 sf0400666851 4 667852 NA 2.21E-06
vg0127316647 sf0127315603 1 27316647 NA 2.90E-06