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 mr1269 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
vg0320879541 sf0320878051 3 20879541 4.88E-07 4.02E-06
vg0607694365 sf0607693366 6 7694365 3.15E-06 6.83E-06
vg0915105890 sf0915104889 9 15105890 5.98E-06 NA
vg0114519177 sf0114518151 1 14519177 6.03E-06 NA
vg0335648847 sf0335641716 3 35648847 NA 6.32E-06