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 mr1075 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
vg0222718166 sf0222712297 2 22718166 2.23E-62 5.03E-24
vg0706909089 sf0706908094 7 6909089 8.13E-34 NA
vg0716014760 sf0716013767 7 16014760 3.83E-33 NA
vg0626803080 sf0626802083 6 26803080 5.00E-33 NA
vg0617630710 sf0617629713 6 17630710 1.31E-32 NA
vg0311698039 sf0311696757 3 11698039 2.71E-29 2.96E-06
vg0222725003 sf0222719134 2 22725003 NA 1.05E-09
vg0223736656 sf0223730787 2 23736656 NA 4.26E-09
vg0715115605 sf0715114612 7 15115605 NA 2.75E-07
vg0222630367 sf0222624498 2 22630367 NA 1.21E-06
vg0222817468 sf0222811599 2 22817468 NA 1.23E-06
vg1112606104 sf1112142307 11 12606104 NA 2.20E-06
vg0506635057 sf0506634998 5 6635057 NA 3.23E-06