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 mr1149 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
vg0135794714 sf0135793671 1 35794714 2.61E-08 NA
vg0123384350 sf0123383306 1 23384350 3.36E-08 NA
vg0313641931 sf0313640648 3 13641931 4.33E-08 NA
vg0432345183 sf0432160072 4 32345183 4.97E-07 2.46E-06
vg0121412555 sf0121411510 1 21412555 NA 1.55E-06