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 mr1939 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
vg0315315801 sf0315314448 3 15315801 5.50E-13 NA
vg0316019263 sf0316017910 3 16019263 1.37E-12 NA
vg1203006745 sf1203005747 12 3006745 1.65E-12 NA
vg0427285532 sf0427100401 4 27285532 4.66E-12 NA
vg0700094945 sf0700093945 7 94945 5.40E-12 NA
vg0800761712 sf0800760714 8 761712 6.45E-12 NA
vg0905696336 sf0905695336 9 5696336 9.79E-10 1.71E-06