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 mr1890 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 1.25E-09 8.11E-08
vg0130689494 sf0130688450 1 30689494 6.88E-09 6.89E-08
vg1104947437 sf1104943248 11 4947437 1.38E-07 1.63E-06
vg1105750981 sf1105746733 11 5750981 1.95E-07 9.89E-07
vg0523235966 sf0523173387 5 23235966 1.02E-06 2.68E-06
vg0712961657 sf0712960664 7 12961657 1.81E-06 4.48E-06
vg0514184495 sf0514127039 5 14184495 2.22E-06 4.01E-06
vg1107276178 sf1107271923 11 7276178 3.99E-06 2.75E-06