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 mr1656 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
vg1117462408 sf1116996263 11 17462408 2.21E-08 3.85E-07
vg0113027848 sf0113026822 1 13027848 1.16E-07 1.11E-06
vg1127790119 sf1127318505 11 27790119 1.38E-07 3.21E-07
vg0423542197 sf0423357054 4 23542197 2.24E-07 5.45E-06
vg0336291923 sf0336284793 3 36291923 3.22E-07 2.09E-06
vg0922881564 sf0922881083 9 22881564 4.60E-07 4.07E-06
vg1218074718 sf1218046154 12 18074718 NA 4.83E-06