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 mr1419 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
vg0323778716 sf0323776890 3 23778716 5.84E-06 3.93E-06
vg0716931364 sf0716930371 7 16931364 NA 1.06E-06
vg0402100710 sf0402096304 4 2100710 NA 2.21E-06
vg0405360103 sf0405355544 4 5360103 NA 4.40E-06
vg0706191493 sf0706190494 7 6191493 NA 4.62E-06
vg1119463807 sf1118997495 11 19463807 NA 7.85E-06