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 mr1563 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
vg0723516704 sf0723515711 7 23516704 5.86E-16 1.69E-16
vg0723388086 sf0723387093 7 23388086 5.88E-11 9.75E-11
vg0140885275 sf0140884232 1 40885275 5.65E-09 5.47E-06
vg0315759840 sf0315758487 3 15759840 3.85E-08 1.13E-07
vg0723474331 sf0723473338 7 23474331 5.52E-08 2.71E-09
vg0125352342 sf0125351298 1 25352342 2.16E-06 2.99E-06
vg0404313730 sf0404309336 4 4313730 2.72E-06 3.40E-06
vg0401360082 sf0401355632 4 1360082 3.37E-06 3.52E-07
vg1218957710 sf1218929145 12 18957710 7.82E-06 3.06E-06
vg0410543704 sf0410534403 4 10543704 NA 1.87E-06