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 mr1216 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
vg0801511665 sf0801510667 8 1511665 4.05E-10 1.34E-06
vg0335517007 sf0335509876 3 35517007 4.95E-08 5.10E-07
vg0919635520 sf0919635110 9 19635520 5.13E-08 NA
vg1002941120 sf1002940097 10 2941120 2.05E-07 1.31E-06
vg1002941211 sf1002940188 10 2941211 3.11E-07 1.21E-06
vg0315064182 sf0315062829 3 15064182 NA 1.93E-06
vg1207826504 sf1207823910 12 7826504 NA 1.95E-06
vg0210574754 sf0210574752 2 10574754 NA 3.19E-06
vg0235593093 sf0235587224 2 35593093 NA 4.38E-06
vg0503840950 sf0503840927 5 3840950 NA 4.50E-06
vg1002881447 sf1002880424 10 2881447 NA 5.45E-06