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 mr1565 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
vg0401118008 sf0401113558 4 1118008 9.04E-17 7.31E-08
vg0401118032 sf0401113582 4 1118032 9.92E-17 2.25E-08
vg0400907136 sf0400906136 4 907136 5.66E-14 1.85E-06
vg0119413705 sf0119412660 1 19413705 1.20E-12 NA
vg0327690029 sf0327683082 3 27690029 1.21E-12 NA
vg0434912939 sf0434727829 4 34912939 1.40E-12 NA
vg0803543650 sf0803542653 8 3543650 6.21E-10 NA
vg0327685371 sf0327678424 3 27685371 2.77E-09 3.52E-06
vg0402387202 sf0402382797 4 2387202 6.87E-09 3.77E-06
vg0208214479 sf0208214478 2 8214479 1.79E-08 NA
vg0614034992 sf0614033993 6 14034992 NA 1.88E-06
vg0913080416 sf0913079415 9 13080416 NA 3.33E-06