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 mr1010 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
vg0621415154 sf0621414157 6 21415154 1.16E-16 NA
vg0621398034 sf0621397037 6 21398034 1.73E-16 3.14E-06
vg0131720791 sf0131719747 1 31720791 3.23E-16 NA
vg0133208220 sf0133207176 1 33208220 4.94E-16 6.84E-07
vg0134658859 sf0134657816 1 34658859 5.76E-16 NA
vg0905150436 sf0905149436 9 5150436 7.45E-16 NA
vg0406358263 sf0406353703 4 6358263 9.98E-16 NA
vg0905326525 sf0905325525 9 5326525 4.80E-14 NA
vg0410038407 sf0410029104 4 10038407 1.56E-13 2.92E-06
vg0621381864 sf0621380867 6 21381864 3.07E-13 NA
vg0725447803 sf0725446809 7 25447803 6.75E-13 NA
vg0525210558 sf0525147979 5 25210558 NA 1.78E-06
vg1215218812 sf1215216109 12 15218812 NA 1.93E-06
vg0528462620 sf0528399975 5 28462620 NA 1.98E-06
vg0303915812 sf0303914808 3 3915812 NA 3.84E-06
vg1209679986 sf1209677395 12 9679986 NA 3.85E-06
vg1012224763 sf1012153578 10 12224763 NA 4.47E-06