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 mr1508 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
vg0225907297 sf0225901428 2 25907297 6.19E-09 1.55E-06
vg0913716234 sf0913715233 9 13716234 1.96E-08 9.69E-06
vg0133084167 sf0133083123 1 33084167 2.56E-08 NA
vg1122665821 sf1122199692 11 22665821 2.63E-08 NA
vg0919712999 sf0919712589 9 19712999 3.92E-08 8.48E-06
vg0208828020 sf0208828018 2 8828020 2.50E-07 4.46E-06