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 mr1425 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
vg1210259194 sf1210256606 12 10259194 6.11E-10 1.48E-06
vg0431840755 sf0431655649 4 31840755 9.03E-10 NA
vg1209064091 sf1209061500 12 9064091 9.52E-10 4.30E-06
vg1209644048 sf1209641457 12 9644048 1.31E-09 3.93E-07
vg0802505868 sf0802504871 8 2505868 2.05E-08 1.56E-06
vg1209219626 sf1209217035 12 9219626 NA 7.97E-07
vg1211273095 sf1211270431 12 11273095 NA 1.54E-06
vg0321870751 sf0321869261 3 21870751 NA 2.52E-06
vg0407628826 sf0407624093 4 7628826 NA 4.39E-06
vg1210267480 sf1210264892 12 10267480 NA 4.49E-06
vg0226196512 sf0226190643 2 26196512 NA 6.19E-06