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 mr1562 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
vg0516853388 sf0516793029 5 16853388 2.53E-09 2.54E-09
vg0517538140 sf0517477783 5 17538140 9.68E-08 9.69E-08
vg0212840665 sf0212840661 2 12840665 7.10E-07 7.08E-07
vg0315231624 sf0315230271 3 15231624 7.33E-07 7.33E-07
vg1127845569 sf1127373955 11 27845569 9.37E-07 9.39E-07
vg0727210166 sf0727209172 7 27210166 1.59E-06 1.58E-06
vg1214046478 sf1214043818 12 14046478 2.95E-06 2.96E-06
vg0415467485 sf0415458170 4 15467485 2.98E-06 2.97E-06
vg1117484883 sf1117018738 11 17484883 3.07E-06 3.07E-06
vg1013275525 sf1013204295 10 13275525 3.50E-06 3.51E-06
vg1111583372 sf1111577689 11 11583372 3.82E-06 3.81E-06
vg1221867400 sf1221833947 12 21867400 4.78E-06 4.79E-06