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 mr1920 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
vg0604742724 sf0604741725 6 4742724 2.73E-19 2.36E-09
vg0604236666 sf0604235667 6 4236666 2.40E-17 3.97E-10
vg0326827276 sf0326820329 3 26827276 1.97E-16 3.67E-07
vg0303967067 sf0303966063 3 3967067 7.40E-15 NA
vg0414221572 sf0414212285 4 14221572 8.76E-15 NA
vg0311146439 sf0311145157 3 11146439 2.07E-14 NA
vg0414275568 sf0414266281 4 14275568 4.24E-14 NA