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 mr1265 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
vg0816082795 sf0816080081 8 16082795 1.11E-07 7.39E-07
vg0507693857 sf0507693798 5 7693857 2.26E-07 1.18E-06
vg1208472022 sf1208469429 12 8472022 2.37E-07 7.47E-07
vg0521819187 sf0521756629 5 21819187 3.57E-07 NA
vg1022985870 sf1022914343 10 22985870 4.23E-07 3.84E-06
vg0622353554 sf0622352557 6 22353554 1.06E-06 2.06E-06
vg1017701953 sf1017630726 10 17701953 2.05E-06 NA
vg1218040492 sf1218011928 12 18040492 NA 2.62E-06
vg1116376902 sf1115911779 11 16376902 NA 4.35E-06