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 mr1073 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
vg0819479739 sf0819477026 8 19479739 5.18E-10 2.41E-07
vg1202732210 sf1202731212 12 2732210 3.26E-09 2.16E-06
vg0721864023 sf0721863030 7 21864023 3.02E-08 9.44E-06
vg0812027729 sf0812026734 8 12027729 5.72E-08 9.24E-06
vg0315136621 sf0315135268 3 15136621 6.56E-08 NA
vg0811525014 sf0811524019 8 11525014 NA 1.02E-06