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 mr1975 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
vg0100929671 sf0100928671 1 929671 5.27E-09 NA
vg0329591755 sf0329584795 3 29591755 8.25E-09 NA
vg1105907484 sf1105903236 11 5907484 1.51E-08 NA
vg0706999938 sf0706998943 7 6999938 1.80E-08 NA
vg0123839187 sf0123838143 1 23839187 1.82E-08 NA
vg0336117363 sf0336110289 3 36117363 7.94E-08 2.00E-06
vg0900764359 sf0900763359 9 764359 6.65E-06 7.19E-06