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 mr1539 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
vg0429856676 sf0429671546 4 29856676 4.82E-10 NA
vg0821161332 sf0821158619 8 21161332 5.35E-10 7.62E-06
vg1017749017 sf1017677790 10 17749017 1.52E-09 NA
vg0619697887 sf0619696890 6 19697887 2.18E-09 NA
vg0818001372 sf0817998659 8 18001372 4.02E-09 NA
vg0428859159 sf0428674014 4 28859159 5.52E-09 NA
vg1208123893 sf1208121299 12 8123893 9.47E-09 4.43E-06
vg0821130902 sf0821128189 8 21130902 1.69E-08 NA
vg0322274602 sf0322273109 3 22274602 7.25E-08 7.65E-06
vg0315264922 sf0315263569 3 15264922 2.58E-06 NA
vg1107330914 sf1107326659 11 7330914 3.85E-06 NA
vg0324101632 sf0324099711 3 24101632 NA 3.52E-06