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 mr1454 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
vg0137876212 sf0137875169 1 37876212 1.29E-19 NA
vg0133341526 sf0133340482 1 33341526 2.54E-19 NA
vg0914464094 sf0914463093 9 14464094 6.23E-19 5.92E-06
vg0914518678 sf0914517677 9 14518678 7.87E-19 9.76E-06
vg0725485552 sf0725484558 7 25485552 1.45E-18 NA
vg0141080827 sf0141079784 1 41080827 1.63E-18 NA
vg0135613639 sf0135612596 1 35613639 4.30E-17 NA
vg0101289411 sf0101288411 1 1289411 1.26E-15 3.09E-06
vg0724760962 sf0724759968 7 24760962 1.08E-14 NA
vg0408423088 sf0408418362 4 8423088 1.25E-14 NA
vg0111846225 sf0111845199 1 11846225 3.69E-14 5.08E-06
vg0210775892 sf0210775890 2 10775892 NA 1.79E-06
vg0405873164 sf0405868605 4 5873164 NA 1.92E-06
vg0623981975 sf0623980978 6 23981975 NA 3.00E-06