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 mr1688 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
vg0709316642 sf0709315648 7 9316642 6.03E-07 6.00E-07
vg0818577556 sf0818574843 8 18577556 1.34E-06 1.34E-06
vg1218873031 sf1218844466 12 18873031 1.36E-06 1.36E-06
vg0909396914 sf0909395913 9 9396914 3.11E-06 3.11E-06
vg0619002190 sf0619001193 6 19002190 3.25E-06 3.26E-06
vg0423538981 sf0423353838 4 23538981 3.56E-06 3.54E-06
vg1103055570 sf1103051474 11 3055570 3.88E-06 3.89E-06
vg0818578468 sf0818575755 8 18578468 4.00E-06 4.00E-06
vg1207495052 sf1207492458 12 7495052 4.14E-06 4.14E-06