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 mr1273 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
vg0527263305 sf0527200661 5 27263305 6.33E-07 6.33E-07
vg0205136369 sf0205136366 2 5136369 1.05E-06 1.05E-06
vg1118352952 sf1117886810 11 18352952 4.46E-06 4.47E-06
vg1118285234 sf1117819093 11 18285234 4.83E-06 4.82E-06
vg0528755805 sf0528693160 5 28755805 4.88E-06 4.88E-06
vg0300255134 sf0300254134 3 255134 9.45E-06 9.45E-06