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 mr1764 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 1.02E-09 1.23E-06
vg0220342715 sf0220336847 2 20342715 3.08E-09 NA
vg0335297514 sf0335290383 3 35297514 5.59E-09 8.90E-06
vg0902107236 sf0902106236 9 2107236 6.61E-09 1.54E-06
vg0801628860 sf0801627862 8 1628860 1.37E-08 NA
vg0805608836 sf0805607839 8 5608836 1.30E-06 8.88E-07
vg0207692645 sf0207692644 2 7692645 NA 2.06E-06
vg0816931318 sf0816928604 8 16931318 NA 2.80E-06