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 mr1249 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
vg0104785744 sf0104784744 1 4785744 6.46E-08 6.46E-08
vg1121442556 sf1120976433 11 21442556 1.78E-07 1.78E-07
vg0826637282 sf0826634568 8 26637282 6.12E-07 6.12E-07
vg0142887146 sf0142886102 1 42887146 6.12E-07 6.12E-07
vg0714973849 sf0714972856 7 14973849 1.25E-06 1.25E-06
vg0115235371 sf0115234345 1 15235371 1.88E-06 1.88E-06
vg0908891812 sf0908890811 9 8891812 1.94E-06 1.94E-06
vg0118067123 sf0118066077 1 18067123 2.89E-06 2.89E-06
vg0900341874 sf0900340874 9 341874 4.07E-06 4.07E-06
vg0800504216 sf0800503216 8 504216 4.91E-06 4.91E-06
vg1108185945 sf1108181690 11 8185945 4.97E-06 4.97E-06