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 mr1896 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
vg0130670983 sf0130669939 1 30670983 5.02E-10 9.19E-08
vg0921387658 sf0921387177 9 21387658 2.30E-09 2.36E-08
vg0128528102 sf0128527057 1 28528102 3.44E-08 NA
vg0706563392 sf0706562397 7 6563392 5.87E-08 7.77E-06
vg0208966807 sf0208966805 2 8966807 9.77E-08 3.50E-06
vg1219821279 sf1219792749 12 19821279 3.27E-07 5.14E-07
vg0225789722 sf0225783853 2 25789722 8.33E-07 3.90E-06
vg0124471054 sf0124470010 1 24471054 1.65E-06 NA