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 mr1341 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
vg0324153872 sf0324151951 3 24153872 3.77E-08 3.77E-08
vg0714470576 sf0714469583 7 14470576 4.92E-08 4.92E-08
vg1000566988 sf1000565964 10 566988 2.76E-07 2.76E-07
vg0314333349 sf0314332038 3 14333349 4.79E-07 4.79E-07
vg0224078729 sf0224072860 2 24078729 5.50E-07 5.50E-07
vg0525250031 sf0525187452 5 25250031 8.71E-07 8.71E-07
vg0306548970 sf0306547970 3 6548970 1.43E-06 1.43E-06
vg0211327135 sf0211327132 2 11327135 1.59E-06 1.59E-06
vg1202061889 sf1202060887 12 2061889 2.43E-06 2.43E-06
vg1208286887 sf1208284293 12 8286887 3.88E-06 3.88E-06
vg0224652507 sf0224646638 2 24652507 3.99E-06 4.00E-06