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 mr1525 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
vg0402459044 sf0402454642 4 2459044 4.50E-11 1.05E-06
vg0401738570 sf0401734169 4 1738570 1.55E-09 2.50E-06
vg0711577817 sf0711576823 7 11577817 4.13E-09 NA
vg0405913502 sf0405908943 4 5913502 6.47E-09 1.09E-08
vg0405536257 sf0405531698 4 5536257 6.99E-09 2.24E-08
vg0405493285 sf0405488726 4 5493285 1.39E-07 9.61E-08
vg0412701691 sf0412692402 4 12701691 2.56E-07 3.51E-06
vg0707566881 sf0707565886 7 7566881 1.18E-06 1.27E-06
vg1217575687 sf1217569642 12 17575687 3.39E-06 3.18E-06