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 mr1448 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
vg0119128220 sf0119127175 1 19128220 1.83E-11 2.79E-07
vg0119127859 sf0119126814 1 19127859 8.98E-11 2.34E-08
vg0327970149 sf0327963203 3 27970149 7.82E-10 7.08E-06
vg0327967882 sf0327960936 3 27967882 2.39E-09 2.47E-06
vg0414675954 sf0414666668 4 14675954 3.21E-08 NA
vg0431306962 sf0431121856 4 31306962 4.49E-08 NA
vg1223653374 sf1223619830 12 23653374 8.34E-08 NA
vg0804990899 sf0804989902 8 4990899 1.53E-07 4.80E-07