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 mr1318 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
vg0502158078 sf0502158053 5 2158078 8.17E-08 8.11E-06
vg1116713051 sf1116247928 11 16713051 5.93E-07 9.41E-07
vg0615411425 sf0615410426 6 15411425 2.03E-06 2.98E-06
vg0810915454 sf0810914459 8 10915454 3.68E-06 7.98E-07
vg0407630134 sf0407625401 4 7630134 6.31E-06 1.51E-06
vg1204900448 sf1204899433 12 4900448 8.10E-06 4.61E-07