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 mr1986 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
vg0600385617 sf0600384617 6 385617 1.31E-08 NA
vg1002941211 sf1002940188 10 2941211 9.25E-08 6.38E-06
vg1223141422 sf1223107882 12 23141422 9.45E-08 NA
vg1121675225 sf1121209102 11 21675225 1.85E-07 3.80E-06
vg0206275287 sf0206275287 2 6275287 2.77E-06 NA
vg0112709868 sf0112708842 1 12709868 4.39E-06 NA
vg0921412406 sf0921411925 9 21412406 5.39E-06 NA