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 mr1970 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
vg0607267655 sf0607266656 6 7267655 1.87E-32 7.58E-20
vg0919836629 sf0919836148 9 19836629 1.40E-13 NA
vg0622190408 sf0622189411 6 22190408 5.32E-13 NA
vg0429319504 sf0429134370 4 29319504 5.75E-13 NA
vg0722528393 sf0722527400 7 22528393 5.05E-12 NA
vg0619887922 sf0619886925 6 19887922 2.51E-11 5.63E-08
vg0334582408 sf0334575278 3 34582408 2.21E-10 1.66E-06
vg0607527077 sf0607526078 6 7527077 1.33E-08 4.08E-07
vg0607310239 sf0607309240 6 7310239 1.70E-08 2.11E-09
vg0621838550 sf0621837553 6 21838550 1.17E-07 1.85E-06
vg0500741833 sf0500741833 5 741833 5.41E-07 4.14E-06
vg0607025833 sf0607024834 6 7025833 NA 4.47E-06