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 mr1141 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
vg0602403184 sf0602402185 6 2403184 6.58E-109 2.09E-28
vg0602397891 sf0602396892 6 2397891 7.00E-109 1.42E-28
vg0602339249 sf0602338250 6 2339249 9.70E-107 1.49E-28
vg0602749885 sf0602748886 6 2749885 3.95E-105 2.11E-28
vg0701792889 sf0701791890 7 1792889 2.92E-52 NA
vg0623816400 sf0623815403 6 23816400 1.60E-50 NA
vg0526848842 sf0526786200 5 26848842 7.76E-50 NA
vg0900635659 sf0900634659 9 635659 3.06E-49 NA
vg1221014609 sf1220981159 12 21014609 NA 5.71E-09
vg1211781305 sf1211778641 12 11781305 NA 9.18E-08
vg0130961428 sf0130960384 1 30961428 NA 1.97E-07
vg0717100285 sf0717099292 7 17100285 NA 6.54E-07
vg1222591917 sf1222558356 12 22591917 NA 6.58E-07
vg0107013970 sf0107012970 1 7013970 NA 1.84E-06
vg0304099620 sf0304098616 3 4099620 NA 2.15E-06
vg1223337361 sf1223303821 12 23337361 NA 2.26E-06
vg0219929533 sf0219923665 2 19929533 NA 2.75E-06
vg1121945630 sf1121479501 11 21945630 NA 3.26E-06
vg0124206667 sf0124205623 1 24206667 NA 4.07E-06
vg0522841594 sf0522779036 5 22841594 NA 4.35E-06
vg1223438680 sf1223405140 12 23438680 NA 4.44E-06
vg1118908807 sf1118442616 11 18908807 NA 4.77E-06