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 mr1059 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
vg0405710877 sf0405706316 4 5710877 3.96E-14 NA
vg0715863001 sf0715862008 7 15863001 6.12E-13 6.02E-07
vg0133158489 sf0133157445 1 33158489 3.13E-12 NA
vg0100547738 sf0100546738 1 547738 5.09E-12 NA
vg0405539066 sf0405534507 4 5539066 1.06E-11 NA
vg0715862869 sf0715861876 7 15862869 1.56E-11 1.06E-07
vg0715381494 sf0715380501 7 15381494 4.43E-10 1.36E-06
vg0413884424 sf0413875142 4 13884424 4.18E-09 NA
vg0619934018 sf0619933021 6 19934018 1.20E-07 NA
vg1209154479 sf1209151888 12 9154479 NA 1.24E-06
vg1015203758 sf1015132526 10 15203758 NA 1.88E-06
vg0404950546 sf0404945985 4 4950546 NA 2.28E-06