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 mr1556 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
vg0805992743 sf0805991746 8 5992743 3.74E-10 6.42E-07
vg0335297514 sf0335290383 3 35297514 7.31E-10 1.85E-06
vg0902107236 sf0902106236 9 2107236 1.91E-09 1.17E-06
vg0801628860 sf0801627862 8 1628860 2.29E-09 7.45E-06
vg0105521069 sf0105520069 1 5521069 3.56E-09 NA
vg0805608836 sf0805607839 8 5608836 7.22E-07 5.71E-07
vg1214134657 sf1214131997 12 14134657 NA 4.17E-06