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 mr1529 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
vg0617644367 sf0617643370 6 17644367 3.85E-07 3.85E-07
vg0100357693 sf0100356693 1 357693 4.46E-07 4.46E-07
vg1009643741 sf1009572562 10 9643741 8.37E-07 8.37E-07
vg0916682401 sf0916681400 9 16682401 2.21E-06 2.21E-06
vg1204379459 sf1204378447 12 4379459 2.66E-06 2.66E-06
vg0103324572 sf0103323572 1 3324572 4.03E-06 4.03E-06
vg0113615961 sf0113614935 1 13615961 4.69E-06 4.69E-06