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 mr1315 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
vg0618125425 sf0618124428 6 18125425 1.03E-09 NA
vg0327979488 sf0327972542 3 27979488 2.82E-09 NA
vg1219410791 sf1219382261 12 19410791 3.28E-09 NA
vg0208850397 sf0208850395 2 8850397 3.97E-09 NA
vg1117585638 sf1117119495 11 17585638 5.88E-09 NA
vg0229806450 sf0229800581 2 29806450 4.80E-08 NA
vg0140479964 sf0140478921 1 40479964 5.95E-08 3.18E-06
vg1018076166 sf1018004937 10 18076166 1.31E-06 NA