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 mr1789 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
vg0204904936 sf0204904933 2 4904936 3.11E-16 NA
vg0311518714 sf0311517432 3 11518714 3.99E-16 NA
vg0414202308 sf0414193024 4 14202308 4.63E-16 NA
vg0122888708 sf0122887664 1 22888708 9.86E-16 NA
vg0125999123 sf0125998079 1 25999123 2.47E-15 NA
vg0409495729 sf0409486427 4 9495729 3.09E-13 NA
vg0117832704 sf0117831658 1 17832704 NA 5.62E-06
vg0124173863 sf0124172819 1 24173863 NA 6.59E-06