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 mr1091 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
vg0610559165 sf0610558166 6 10559165 4.96E-131 5.78E-45
vg0610584498 sf0610583499 6 10584498 1.21E-97 5.25E-35
vg0617223679 sf0617222682 6 17223679 1.34E-66 4.42E-10
vg0614169262 sf0614168263 6 14169262 4.48E-62 8.44E-08
vg0719209059 sf0719208066 7 19209059 1.03E-60 NA
vg0233406552 sf0233400683 2 33406552 5.67E-59 NA
vg0629122299 sf0629121301 6 29122299 1.45E-54 5.70E-09
vg0610476284 sf0610475285 6 10476284 NA 1.06E-20
vg0610763769 sf0610762770 6 10763769 NA 1.39E-20
vg0610679715 sf0610678716 6 10679715 NA 3.51E-18
vg0610444069 sf0610443070 6 10444069 NA 3.00E-15
vg0611682950 sf0611681951 6 11682950 NA 1.52E-14
vg0610813890 sf0610812891 6 10813890 NA 8.81E-12
vg0610212566 sf0610211567 6 10212566 NA 1.45E-11
vg0609889743 sf0609888744 6 9889743 NA 2.31E-11
vg0611926589 sf0611925590 6 11926589 NA 8.85E-11
vg0610069930 sf0610068931 6 10069930 NA 2.63E-10
vg0609647029 sf0609646030 6 9647029 NA 2.08E-09
vg0206168898 sf0206168898 2 6168898 NA 6.27E-09
vg0610116533 sf0610115534 6 10116533 NA 1.14E-08
vg0610488848 sf0610487849 6 10488848 NA 2.88E-08
vg0610929434 sf0610928435 6 10929434 NA 3.28E-08
vg0609665338 sf0609664339 6 9665338 NA 7.91E-08
vg0610027827 sf0610026828 6 10027827 NA 9.27E-08
vg0612050111 sf0612049112 6 12050111 NA 9.56E-08
vg0615515353 sf0615514355 6 15515353 NA 9.95E-08
vg0610034523 sf0610033524 6 10034523 NA 1.15E-07
vg0222739831 sf0222733962 2 22739831 NA 6.86E-06