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 mr1915 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
vg0715682872 sf0715681879 7 15682872 1.50E-10 7.78E-07
vg1209657848 sf1209655257 12 9657848 5.32E-10 NA
vg0727546013 sf0727545019 7 27546013 1.83E-09 NA
vg0406835467 sf0406830912 4 6835467 1.83E-09 NA
vg0622963600 sf0622962603 6 22963600 2.15E-09 NA
vg0712046729 sf0712045735 7 12046729 3.04E-09 4.96E-06
vg0525628187 sf0525565608 5 25628187 8.57E-09 NA
vg0727008459 sf0727007465 7 27008459 1.01E-08 2.77E-06
vg0812330953 sf0812329958 8 12330953 1.07E-08 4.27E-07