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 mr1245 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
vg0222337580 sf0222331711 2 22337580 6.29E-08 6.29E-08
vg0819431872 sf0819429159 8 19431872 3.27E-07 3.27E-07
vg0321576069 sf0321574579 3 21576069 4.25E-07 4.25E-07
vg0219780702 sf0219774834 2 19780702 1.36E-06 1.36E-06
vg0221872696 sf0221866827 2 21872696 2.37E-06 2.37E-06
vg0107079035 sf0107078035 1 7079035 3.37E-06 3.37E-06
vg0901536547 sf0901535547 9 1536547 4.60E-06 4.60E-06
vg0417258890 sf0417086931 4 17258890 4.93E-06 4.93E-06