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 mr1893 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
vg0116423916 sf0116422890 1 16423916 1.81E-08 7.89E-07
vg1200051954 sf1200050954 12 51954 2.10E-08 9.52E-07
vg0909793368 sf0909792367 9 9793368 1.96E-07 1.60E-06
vg1128247542 sf1127724321 11 28247542 2.84E-07 1.71E-06
vg1103187142 sf1103183045 11 3187142 5.34E-07 1.82E-07
vg1113029322 sf1112565643 11 13029322 6.75E-07 1.72E-06
vg0107614928 sf0107613928 1 7614928 6.47E-06 3.43E-06
vg0129007811 sf0129006766 1 29007811 8.83E-06 3.84E-07
vg0318700362 sf0318699122 3 18700362 NA 1.16E-06
vg1123693924 sf1123227794 11 23693924 NA 4.44E-06