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 mr1711 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
vg0114410620 sf0114409594 1 14410620 3.53E-69 NA
vg0321455590 sf0321454100 3 21455590 4.51E-68 8.83E-06
vg0305537429 sf0305536429 3 5537429 1.51E-67 NA
vg0113971432 sf0113970406 1 13971432 1.60E-67 1.31E-06
vg0321535444 sf0321533954 3 21535444 2.97E-67 5.93E-06
vg0321533209 sf0321531719 3 21533209 5.33E-67 3.79E-06
vg0917746484 sf0917745483 9 17746484 1.14E-66 NA
vg0914933853 sf0914932852 9 14933853 1.20E-66 NA
vg0917927607 sf0917926606 9 17927607 2.24E-62 6.45E-07
vg0519030720 sf0518968204 5 19030720 NA 1.69E-06
vg0900683858 sf0900682858 9 683858 NA 2.39E-06
vg0139609782 sf0139608739 1 39609782 NA 3.30E-06
vg0822837877 sf0822835164 8 22837877 NA 3.54E-06
vg0910450391 sf0910449390 9 10450391 NA 3.55E-06
vg0116844307 sf0116843281 1 16844307 NA 4.39E-06