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 mr1796 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
vg1006757388 sf1006773011 10 6757388 4.42E-07 4.42E-07
vg1122197777 sf1121731648 11 22197777 8.69E-07 8.70E-07
vg0610073622 sf0610072623 6 10073622 1.53E-06 1.53E-06
vg1220123744 sf1220095186 12 20123744 2.92E-06 2.92E-06
vg1015851728 sf1015780498 10 15851728 3.02E-06 3.02E-06
vg1125279847 sf1124813687 11 25279847 3.79E-06 3.79E-06