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 mr1063 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
vg0316205466 sf0316204114 3 16205466 1.53E-09 NA
vg0141852317 sf0141851274 1 41852317 2.33E-09 NA
vg0203336657 sf0203336655 2 3336657 8.37E-09 NA
vg1100795910 sf1100794911 11 795910 1.67E-08 NA
vg0712717909 sf0712716916 7 12717909 1.75E-08 NA
vg0431889500 sf0431704395 4 31889500 8.81E-07 NA
vg0713015396 sf0713014403 7 13015396 9.46E-07 8.44E-06
vg0714148441 sf0714147448 7 14148441 1.07E-06 NA
vg0118996593 sf0118995548 1 18996593 4.75E-06 NA
vg1117477788 sf1117011643 11 17477788 8.41E-06 NA