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 mr1281 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
vg0725325993 sf0725324999 7 25325993 1.76E-07 1.76E-07
vg0224530358 sf0224524489 2 24530358 7.22E-07 7.22E-07
vg1005268365 sf1005284902 10 5268365 7.46E-07 7.46E-07
vg1012299970 sf1012228785 10 12299970 1.04E-06 1.04E-06
vg0620515026 sf0620514029 6 20515026 1.31E-06 1.31E-06
vg0208191413 sf0208191412 2 8191413 1.47E-06 1.47E-06
vg0618487499 sf0618486502 6 18487499 1.64E-06 1.64E-06