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 mr1633 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
vg0205292054 sf0205292052 2 5292054 6.11E-12 2.65E-10
vg0205301629 sf0205301628 2 5301629 1.56E-11 1.00E-10
vg0726964336 sf0726963342 7 26964336 6.78E-09 NA
vg0709448532 sf0709447538 7 9448532 2.94E-07 1.12E-06
vg0402168068 sf0402163663 4 2168068 6.06E-07 1.25E-07
vg0607980337 sf0607979338 6 7980337 7.41E-06 NA