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 mr1895 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
vg0212840665 sf0212840661 2 12840665 1.59E-06 3.30E-06
vg1221401988 sf1221368535 12 21401988 3.47E-06 1.01E-06
vg0131955794 sf0131954750 1 31955794 4.52E-06 NA
vg1125225153 sf1124758993 11 25225153 NA 2.58E-06
vg1222438639 sf1222405078 12 22438639 NA 3.99E-06
vg0105191165 sf0105190165 1 5191165 NA 4.52E-06