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 mr1648 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
vg1119522374 sf1119056062 11 19522374 3.54E-08 1.09E-06
vg0528383763 sf0528321118 5 28383763 4.22E-07 NA
vg0310120689 sf0310119625 3 10120689 7.52E-07 2.43E-06
vg0523603480 sf0523540901 5 23603480 1.20E-06 NA
vg0403314769 sf0403310372 4 3314769 7.80E-06 NA
vg1125364222 sf1124898062 11 25364222 NA 3.60E-06