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 mr1368 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
vg0204460555 sf0204460552 2 4460555 4.16E-13 2.69E-06
vg1019228502 sf1019157058 10 19228502 1.43E-12 NA
vg0629855440 sf0629854442 6 29855440 3.21E-12 NA
vg0217837493 sf0217831624 2 17837493 5.82E-12 NA
vg0516426471 sf0516368953 5 16426471 1.77E-11 NA
vg0818058241 sf0818055528 8 18058241 1.41E-09 NA
vg0505852417 sf0505852355 5 5852417 NA 1.73E-06
vg1218874242 sf1218845677 12 18874242 NA 4.97E-06
vg1217487071 sf1217481026 12 17487071 NA 8.89E-06