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 mr1713 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
vg1019343853 sf1019272408 10 19343853 3.82E-16 1.23E-07
vg0133425349 sf0133424305 1 33425349 4.93E-15 NA
vg0142135633 sf0142134590 1 42135633 1.06E-14 NA
vg0305022063 sf0305021065 3 5022063 2.81E-14 7.34E-06
vg0423663984 sf0423478841 4 23663984 3.19E-14 NA
vg1002316286 sf1002315263 10 2316286 NA 9.59E-07
vg0501905548 sf0501905530 5 1905548 NA 4.77E-06