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 mr1654 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
vg0113519142 sf0113518116 1 13519142 7.07E-14 NA
vg0306923245 sf0306922243 3 6923245 1.44E-11 NA
vg0119910417 sf0119909372 1 19910417 1.55E-11 NA
vg0114124547 sf0114123521 1 14124547 3.39E-11 NA
vg0802102126 sf0802101129 8 2102126 3.82E-11 NA
vg0119914665 sf0119913620 1 19914665 2.86E-10 NA
vg0112359307 sf0112358281 1 12359307 2.96E-10 1.82E-06
vg0202449000 sf0202448998 2 2449000 8.25E-08 NA
vg0811940095 sf0811939100 8 11940095 9.92E-08 NA
vg0114538326 sf0114537300 1 14538326 2.94E-07 NA