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 mr1952 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
vg0427439811 sf0427254675 4 27439811 5.17E-14 4.90E-06
vg0109565540 sf0109564516 1 9565540 4.80E-12 NA
vg0517675103 sf0517614744 5 17675103 5.92E-12 NA
vg0431444640 sf0431259538 4 31444640 2.56E-11 NA
vg0801792763 sf0801791766 8 1792763 2.77E-11 NA
vg1208631130 sf1208628537 12 8631130 2.42E-08 NA
vg0321576069 sf0321574579 3 21576069 5.73E-08 1.37E-06
vg0517629183 sf0517568825 5 17629183 NA 4.58E-06