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 mr1908 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
vg0122438429 sf0122437384 1 22438429 4.16E-12 1.94E-07
vg0122443930 sf0122442885 1 22443930 4.91E-12 1.61E-07
vg1117255997 sf1116789849 11 17255997 5.66E-09 NA
vg1125582889 sf1125116728 11 25582889 5.80E-09 NA
vg0221209303 sf0221203435 2 21209303 1.54E-08 NA
vg1126586760 sf1126115175 11 26586760 2.04E-08 NA
vg1126584071 sf1126112486 11 26584071 9.24E-08 4.80E-06
vg0105148196 sf0105147196 1 5148196 9.82E-07 NA
vg0122441794 sf0122440749 1 22441794 NA 1.38E-08
vg0608717202 sf0608716203 6 8717202 NA 1.80E-06