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 mr1954 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
vg0609680876 sf0609679877 6 9680876 3.61E-08 NA
vg0920309583 sf0920309102 9 20309583 9.15E-08 NA
vg1218540256 sf1218511692 12 18540256 1.53E-06 NA
vg0900280117 sf0900279117 9 280117 NA 6.78E-07
vg0502701393 sf0502701369 5 2701393 NA 6.86E-06