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 mr1466 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
vg1214703763 sf1214701104 12 14703763 3.79E-07 3.80E-07
vg0918774898 sf0918773898 9 18774898 6.10E-07 6.10E-07
vg0805900956 sf0805899959 8 5900956 1.69E-06 1.69E-06
vg0904643511 sf0904642511 9 4643511 2.16E-06 2.16E-06
vg0810864582 sf0810863587 8 10864582 2.44E-06 2.44E-06
vg0139835584 sf0139834541 1 39835584 2.60E-06 2.60E-06
vg0426438693 sf0426253566 4 26438693 3.27E-06 3.27E-06
vg1124247036 sf1123780906 11 24247036 3.72E-06 3.73E-06
vg0401647520 sf0401643069 4 1647520 4.03E-06 4.03E-06
vg1001247868 sf1001246845 10 1247868 4.13E-06 4.14E-06
vg0211516195 sf0211516191 2 11516195 4.50E-06 4.50E-06
vg0810822568 sf0810821573 8 10822568 4.87E-06 4.87E-06