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 mr1340 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
vg0132416363 sf0132415319 1 32416363 5.11E-07 5.11E-07
vg0406993809 sf0406989080 4 6993809 9.79E-07 9.79E-07
vg0910768444 sf0910767443 9 10768444 1.07E-06 1.07E-06
vg1107376701 sf1107372446 11 7376701 1.15E-06 1.15E-06
vg0200643756 sf0200643756 2 643756 1.30E-06 1.30E-06
vg0314861492 sf0314860139 3 14861492 1.42E-06 1.42E-06
vg0715903365 sf0715902372 7 15903365 2.18E-06 2.18E-06
vg1218273231 sf1218244667 12 18273231 2.96E-06 2.96E-06
vg1218063743 sf1218035179 12 18063743 2.96E-06 2.96E-06
vg0527138870 sf0527076226 5 27138870 3.13E-06 3.13E-06
vg0406995198 sf0406990469 4 6995198 3.34E-06 3.34E-06
vg1112803368 sf1112339689 11 12803368 4.43E-06 4.43E-06
vg0804126025 sf0804125028 8 4126025 4.72E-06 4.72E-06
vg1207348516 sf1207345923 12 7348516 4.82E-06 4.82E-06