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 mr1058 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
vg1013275525 sf1013204295 10 13275525 9.46E-13 8.12E-09
vg0315367085 sf0315365732 3 15367085 3.50E-10 NA
vg0205764374 sf0205764374 2 5764374 4.25E-10 NA
vg0416401038 sf0416229077 4 16401038 6.42E-10 5.73E-06
vg0205960798 sf0205960798 2 5960798 8.10E-10 2.13E-06
vg0522293773 sf0522231214 5 22293773 1.13E-07 NA
vg1213935504 sf1213932842 12 13935504 7.88E-07 9.69E-06