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 mr1357 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
vg0820865298 sf0820862585 8 20865298 5.50E-07 5.50E-07
vg0431411704 sf0431226602 4 31411704 7.49E-07 7.49E-07
vg0130290451 sf0130289406 1 30290451 1.16E-06 1.17E-06
vg0207854825 sf0207854824 2 7854825 1.18E-06 1.18E-06
vg0207908595 sf0207908594 2 7908595 1.78E-06 1.78E-06
vg1107375253 sf1107370998 11 7375253 2.24E-06 2.24E-06
vg0709984451 sf0709983457 7 9984451 2.38E-06 2.38E-06
vg1210206055 sf1210203466 12 10206055 2.71E-06 2.71E-06
vg1104978992 sf1104974803 11 4978992 2.83E-06 2.83E-06
vg0431614108 sf0431429003 4 31614108 2.98E-06 2.98E-06
vg1219593314 sf1219564784 12 19593314 3.27E-06 3.27E-06
vg1007900043 sf1007915653 10 7900043 3.78E-06 3.78E-06
vg0300249514 sf0300248514 3 249514 4.92E-06 4.92E-06