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 mr1520 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
vg1122375960 sf1121909831 11 22375960 2.99E-07 2.99E-07
vg0718951893 sf0718950900 7 18951893 6.89E-07 6.90E-07
vg0414207803 sf0414198519 4 14207803 8.06E-07 8.06E-07
vg1016425716 sf1016354490 10 16425716 1.61E-06 1.61E-06
vg0620536797 sf0620535800 6 20536797 1.91E-06 1.91E-06
vg1002370671 sf1002369648 10 2370671 2.15E-06 2.15E-06
vg0103131279 sf0103130279 1 3131279 2.63E-06 2.63E-06