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 mr1950 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
vg0701536026 sf0701535026 7 1536026 3.12E-18 NA
vg0607246796 sf0607245797 6 7246796 7.75E-18 NA
vg0223111485 sf0223105616 2 23111485 1.09E-17 NA
vg0612665218 sf0612664219 6 12665218 1.76E-17 NA
vg0433404240 sf0433219129 4 33404240 3.21E-17 NA
vg0433199442 sf0433014330 4 33199442 9.99E-17 3.04E-06
vg0916300567 sf0916299566 9 16300567 1.27E-14 NA
vg0430646747 sf0430461622 4 30646747 4.41E-14 NA
vg1015203758 sf1015132526 10 15203758 NA 3.81E-07
vg0421013459 sf0420841512 4 21013459 NA 1.21E-06
vg0714349436 sf0714348443 7 14349436 NA 2.54E-06
vg1206349677 sf1206348567 12 6349677 NA 3.82E-06
vg0404403925 sf0404399529 4 4403925 NA 4.46E-06
vg1206352243 sf1206351133 12 6352243 NA 7.72E-06
vg1212822297 sf1212819636 12 12822297 NA 9.04E-06