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 mr1316 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
vg0514011016 sf0513953560 5 14011016 4.04E-07 1.82E-07
vg0202718323 sf0202718321 2 2718323 7.07E-07 4.60E-06
vg0213822498 sf0213816628 2 13822498 1.59E-06 6.16E-07
vg0528094916 sf0528032271 5 28094916 3.95E-06 NA
vg1106375766 sf1106371518 11 6375766 4.11E-06 2.68E-06
vg0823213341 sf0823210628 8 23213341 6.43E-06 1.10E-06