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 mr1946 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
vg0138649724 sf0138648681 1 38649724 1.24E-10 5.15E-08
vg0138544734 sf0138543691 1 38544734 1.70E-10 2.83E-07
vg0433516710 sf0433331595 4 33516710 6.56E-10 7.61E-08
vg0232298835 sf0232292966 2 32298835 1.14E-09 8.73E-08
vg0231867258 sf0231861389 2 31867258 2.34E-09 1.40E-09
vg0118482824 sf0118481778 1 18482824 2.49E-08 5.26E-06
vg0232543553 sf0232537684 2 32543553 3.42E-08 4.18E-07
vg0818644712 sf0818641999 8 18644712 8.58E-08 9.21E-06