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 mr1612 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
vg0302254076 sf0302253072 3 2254076 7.15E-08 4.03E-06
vg0431411704 sf0431226602 4 31411704 8.46E-08 9.35E-07
vg1204418714 sf1204417702 12 4418714 4.45E-07 8.45E-07
vg0525571394 sf0525508815 5 25571394 7.14E-07 4.60E-06
vg0525927552 sf0525864973 5 25927552 2.45E-06 NA
vg0405830585 sf0405826024 4 5830585 2.92E-06 6.27E-06
vg0404220455 sf0404216059 4 4220455 8.19E-06 2.84E-06