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 mr1676 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
vg0106977787 sf0106976787 1 6977787 9.31E-15 5.12E-09
vg0107022440 sf0107021440 1 7022440 2.93E-14 4.99E-09
vg0235867717 sf0235861848 2 35867717 6.29E-11 NA
vg0808373173 sf0808372177 8 8373173 1.67E-10 5.61E-06
vg0311834985 sf0311833703 3 11834985 1.69E-10 NA
vg0127074848 sf0127073804 1 27074848 2.06E-10 NA
vg0605440179 sf0605439180 6 5440179 7.00E-10 2.08E-06
vg0135077792 sf0135076749 1 35077792 2.99E-08 NA
vg1221699222 sf1221665769 12 21699222 9.09E-07 4.84E-06
vg0516438728 sf0516381210 5 16438728 1.68E-06 8.00E-07
vg0130331339 sf0130330295 1 30331339 2.91E-06 5.27E-07
vg0322267088 sf0322265595 3 22267088 NA 7.29E-07