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 mr1047 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
vg1006757388 sf1006773011 10 6757388 5.66E-09 5.21E-06
vg0910031361 sf0910030360 9 10031361 1.15E-08 9.30E-06
vg0610049736 sf0610048737 6 10049736 1.38E-08 2.53E-06
vg0408114436 sf0408109710 4 8114436 5.64E-08 NA
vg0413262397 sf0413253107 4 13262397 6.41E-08 NA
vg0728682231 sf0728681239 7 28682231 2.64E-07 NA