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 mr1251 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
vg0216569039 sf0216563169 2 16569039 1.93E-14 5.63E-07
vg1018570054 sf1018498611 10 18570054 1.11E-12 NA
vg1000625785 sf1000624761 10 625785 1.30E-12 7.61E-06
vg0417021326 sf0416849368 4 17021326 1.42E-12 NA
vg1219997122 sf1219968564 12 19997122 3.72E-12 NA