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 mr1619 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
vg0406526555 sf0406521998 4 6526555 4.93E-91 1.63E-15
vg0406561841 sf0406557284 4 6561841 2.71E-90 1.51E-14
vg1016495687 sf1016424460 10 16495687 7.67E-75 NA
vg0305429357 sf0305428357 3 5429357 9.32E-75 NA
vg0411678579 sf0411669287 4 11678579 2.18E-74 NA
vg0122842459 sf0122841415 1 22842459 3.45E-73 NA
vg0614107939 sf0614106940 6 14107939 1.15E-72 1.59E-07
vg0521967722 sf0521905164 5 21967722 8.26E-66 1.60E-08
vg0406521772 sf0406517215 4 6521772 NA 8.90E-08
vg0222725881 sf0222720012 2 22725881 NA 1.17E-07
vg1009567423 sf1009496244 10 9567423 NA 1.25E-06
vg0324327479 sf0324325558 3 24327479 NA 3.89E-06
vg0211778650 sf0211778646 2 11778650 NA 6.46E-06