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 mr1260 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
vg0617359224 sf0617358227 6 17359224 6.26E-09 NA
vg0335427772 sf0335420641 3 35427772 8.84E-09 NA
vg0612914787 sf0612913788 6 12914787 2.04E-08 NA
vg1107383686 sf1107379431 11 7383686 3.14E-08 2.15E-06
vg0609676503 sf0609675504 6 9676503 3.72E-08 NA
vg0207762978 sf0207762977 2 7762978 7.12E-07 NA
vg0600619985 sf0600618986 6 619985 1.50E-06 NA
vg0900074355 sf0900073355 9 74355 2.17E-06 NA
vg0810529886 sf0810528890 8 10529886 4.20E-06 5.90E-07
vg1128222970 sf1127699749 11 28222970 4.64E-06 NA