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 mr1775 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
vg1127176280 sf1126704667 11 27176280 9.14E-08 8.91E-08
vg1128379239 sf1127856018 11 28379239 1.95E-07 1.83E-06
vg1007764381 sf1007779991 10 7764381 3.42E-07 3.72E-07
vg0826159919 sf0826157205 8 26159919 5.15E-07 1.43E-07
vg0507301196 sf0507301138 5 7301196 1.01E-06 1.07E-06
vg0313064084 sf0313062802 3 13064084 NA 3.11E-06