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 mr1641 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
vg0205296507 sf0205296506 2 5296507 4.95E-11 3.34E-08
vg0205292202 sf0205292200 2 5292202 5.56E-11 3.28E-08
vg0134092893 sf0134091849 1 34092893 8.39E-08 NA
vg1117584893 sf1117118750 11 17584893 9.20E-08 7.62E-06
vg0332544561 sf0332537434 3 32544561 1.02E-06 7.61E-07
vg0916567594 sf0916566593 9 16567594 8.49E-06 NA