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 mr1816 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
vg0102103204 sf0102102204 1 2103204 5.55E-08 5.63E-06
vg0223525077 sf0223519208 2 23525077 9.84E-08 2.06E-06
vg0805992743 sf0805991746 8 5992743 3.23E-07 NA
vg0607825724 sf0607824725 6 7825724 5.83E-06 NA
vg0621412586 sf0621411589 6 21412586 5.91E-06 2.45E-06
vg0902278490 sf0902277490 9 2278490 NA 1.05E-06
vg0816931318 sf0816928604 8 16931318 NA 2.87E-06