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 mr1428 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
vg0123716192 sf0123715148 1 23716192 4.67E-10 NA
vg0119708645 sf0119707600 1 19708645 1.47E-09 NA
vg0300252316 sf0300251316 3 252316 2.23E-09 NA
vg0914165809 sf0914164808 9 14165809 2.57E-09 NA
vg0119676181 sf0119675136 1 19676181 2.66E-09 NA
vg0138428840 sf0138427797 1 38428840 3.61E-09 NA
vg1210023832 sf1210021243 12 10023832 1.34E-07 1.63E-06
vg0133158830 sf0133157786 1 33158830 1.73E-07 NA
vg0527149984 sf0525898352 5 27149984 7.89E-07 NA
vg0422652665 sf0422467548 4 22652665 1.48E-06 NA
vg0335145372 sf0335138241 3 35145372 2.30E-06 NA