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 mr1733 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
vg0304916283 sf0304915285 3 4916283 1.51E-09 4.53E-06
vg0219185129 sf0219179261 2 19185129 7.12E-09 9.16E-06
vg0315769551 sf0315768198 3 15769551 1.10E-08 3.47E-06
vg0218949150 sf0218943281 2 18949150 1.94E-08 NA
vg0918948219 sf0918947219 9 18948219 3.25E-08 NA
vg0218913885 sf0218908016 2 18913885 3.33E-08 NA
vg0528097115 sf0528034470 5 28097115 7.34E-07 NA