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 mr1391 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
vg0414114398 sf0414105113 4 14114398 1.37E-08 1.37E-08
vg0319086476 sf0319085236 3 19086476 9.26E-08 9.26E-08
vg1223873919 sf1223840372 12 23873919 1.21E-07 1.21E-07
vg0709984451 sf0709983457 7 9984451 6.90E-07 6.90E-07
vg1210406437 sf1210403850 12 10406437 8.09E-07 8.09E-07
vg0416113157 sf0415941190 4 16113157 1.48E-06 1.48E-06