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 mr1072 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
vg0222742213 sf0222736344 2 22742213 4.98E-67 2.27E-27
vg0222723992 sf0222718123 2 22723992 1.89E-66 2.18E-27
vg0705306091 sf0705305092 7 5306091 5.88E-32 NA
vg0626803080 sf0626802083 6 26803080 5.84E-31 NA
vg0407275609 sf0407270879 4 7275609 9.43E-31 4.45E-06
vg0623150078 sf0623149081 6 23150078 2.52E-30 NA
vg0407333553 sf0407328823 4 7333553 3.87E-30 2.78E-06
vg0222857256 sf0222851387 2 22857256 3.60E-28 3.44E-08
vg0222725003 sf0222719134 2 22725003 NA 1.27E-11
vg0222817468 sf0222811599 2 22817468 NA 4.02E-08
vg0223721789 sf0223715920 2 23721789 NA 5.06E-08
vg0224242820 sf0224236951 2 24242820 NA 1.06E-06
vg0226049138 sf0226043269 2 26049138 NA 3.31E-06
vg0224275719 sf0224269850 2 24275719 NA 3.76E-06
vg0506635057 sf0506634998 5 6635057 NA 4.23E-06
vg0315366561 sf0315365208 3 15366561 NA 5.43E-06