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 mr1330 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
vg0114097925 sf0114096899 1 14097925 3.18E-08 1.02E-06
vg0504429178 sf0504429155 5 4429178 7.17E-08 7.23E-07
vg0103426681 sf0103425681 1 3426681 1.97E-07 2.90E-06
vg0315672405 sf0315671052 3 15672405 1.51E-06 9.40E-07
vg0622508179 sf0622507182 6 22508179 5.55E-06 1.89E-06