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 mr1723 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
vg0333220949 sf0333213819 3 33220949 2.47E-62 9.07E-25
vg0329592660 sf0329585700 3 29592660 1.49E-39 NA
vg0231203195 sf0231197326 2 31203195 1.83E-38 NA
vg0915709539 sf0915708538 9 15709539 7.60E-38 NA
vg0719640462 sf0719639469 7 19640462 4.11E-37 NA
vg0333506199 sf0333499069 3 33506199 NA 3.14E-09
vg0332500781 sf0332493654 3 32500781 NA 5.57E-09
vg0700664294 sf0700663294 7 664294 NA 2.09E-07
vg0333300441 sf0333293311 3 33300441 NA 4.26E-07
vg0323951924 sf0323950098 3 23951924 NA 6.80E-07
vg0435030430 sf0434845318 4 35030430 NA 1.15E-06
vg1004652594 sf1004669131 10 4652594 NA 1.34E-06
vg0131504924 sf0131503880 1 31504924 NA 2.51E-06
vg1004627303 sf1004643841 10 4627303 NA 3.36E-06
vg0624955380 sf0624954383 6 24955380 NA 3.40E-06
vg0100916093 sf0100915093 1 916093 NA 4.07E-06