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 mr1986 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
vg1122510926 sf1122044797 11 22510926 5.23E-13 NA
vg0722814740 sf0722813747 7 22814740 2.27E-12 NA
vg1006976423 sf1006992046 10 6976423 2.60E-12 NA
vg0600130622 sf0600129622 6 130622 5.57E-12 NA
vg0518701430 sf0518638913 5 18701430 6.41E-12 NA
vg1122503059 sf1122036930 11 22503059 8.07E-12 NA
vg1121670141 sf1121204018 11 21670141 3.10E-09 1.33E-06
vg1005297414 sf1005313951 10 5297414 1.12E-08 NA
vg0921412406 sf0921411925 9 21412406 NA 2.30E-06
vg0806074323 sf0806073328 8 6074323 NA 3.11E-06
vg0713891127 sf0713890134 7 13891127 NA 5.39E-06