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 mr1860 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
vg0317658313 sf0317657095 3 17658313 1.68E-09 1.12E-08
vg1205542061 sf1205541047 12 5542061 3.90E-08 1.21E-06
vg1110417102 sf1110411647 11 10417102 5.33E-07 1.50E-06
vg0617621070 sf0617620073 6 17621070 1.19E-06 3.29E-06
vg0503273281 sf0503273257 5 3273281 2.79E-06 3.33E-06
vg1110000666 sf1109995243 11 10000666 3.82E-06 4.11E-06