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 mr1552 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
vg0310908621 sf0310907339 3 10908621 2.11E-27 NA
vg0520178846 sf0520116319 5 20178846 2.16E-25 NA
vg0709499311 sf0709498317 7 9499311 3.19E-25 1.11E-06
vg0312020858 sf0312019576 3 12020858 5.09E-25 4.56E-06
vg0608756076 sf0608755077 6 8756076 7.18E-25 NA
vg0917191900 sf0917190899 9 17191900 3.29E-24 NA
vg0132758241 sf0132757197 1 32758241 9.25E-18 NA
vg0512327313 sf0512327243 5 12327313 NA 2.10E-07
vg0819470898 sf0819468185 8 19470898 NA 7.79E-07
vg0609332559 sf0609331560 6 9332559 NA 1.30E-06
vg0605857206 sf0605856207 6 5857206 NA 1.63E-06
vg0626710676 sf0626709679 6 26710676 NA 3.42E-06
vg1016835792 sf1016764564 10 16835792 NA 3.42E-06
vg0912279302 sf0912278301 9 12279302 NA 4.10E-06