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 mr1372 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
vg1104978992 sf1104974803 11 4978992 4.11E-08 4.11E-08
vg1215178307 sf1215175643 12 15178307 1.82E-07 1.82E-07
vg0820888052 sf0820885339 8 20888052 2.19E-07 2.19E-07
vg1105269119 sf1105264870 11 5269119 3.95E-07 3.95E-07
vg0431411704 sf0431226602 4 31411704 5.09E-07 5.09E-07
vg0431655631 sf0431470524 4 31655631 5.30E-07 5.30E-07
vg0431472905 sf0431287803 4 31472905 5.55E-07 5.55E-07
vg0709984451 sf0709983457 7 9984451 1.22E-06 1.22E-06
vg1210705918 sf1210703331 12 10705918 1.46E-06 1.47E-06
vg0130290451 sf0130289406 1 30290451 2.28E-06 2.28E-06
vg0300249514 sf0300248514 3 249514 4.09E-06 4.09E-06
vg1020952242 sf1020880721 10 20952242 4.41E-06 4.41E-06