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 mr1833 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
vg0805946030 sf0805945033 8 5946030 2.73E-09 2.89E-07
vg0124420479 sf0124419435 1 24420479 1.03E-08 1.75E-06
vg0321576069 sf0321574579 3 21576069 1.76E-08 9.74E-07
vg1020531763 sf1020460242 10 20531763 8.21E-08 9.79E-07
vg0329703696 sf0329696736 3 29703696 1.30E-07 4.01E-06
vg0610852582 sf0610851583 6 10852582 5.95E-07 2.85E-06
vg0718397736 sf0718396743 7 18397736 NA 4.84E-06