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 mr1363 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
vg0401608764 sf0401604313 4 1608764 3.63E-08 2.14E-06
vg0516129780 sf0516072264 5 16129780 4.64E-08 2.06E-06
vg0714390906 sf0714389913 7 14390906 1.85E-07 3.91E-07
vg1207511374 sf1207508780 12 7511374 NA 3.46E-06
vg1206604650 sf1206603540 12 6604650 NA 4.41E-06