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 mr1751 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
vg0401647520 sf0401643069 4 1647520 2.32E-07 1.08E-06
vg0428801373 sf0428616223 4 28801373 8.67E-07 NA
vg0414223208 sf0414213921 4 14223208 5.90E-06 NA
vg0223248427 sf0223242558 2 23248427 NA 4.49E-08
vg1223039351 sf1223005811 12 23039351 NA 3.32E-06
vg0208428122 sf0208428121 2 8428122 NA 3.91E-06