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 mr1796 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
vg0201096474 sf0201096474 2 1096474 9.55E-10 NA
vg0701536585 sf0701535585 7 1536585 1.50E-09 NA
vg0227106783 sf0227100914 2 27106783 1.85E-09 2.08E-07
vg0920174968 sf0920174487 9 20174968 2.08E-09 NA
vg0618509091 sf0618508094 6 18509091 2.10E-09 NA
vg0403058985 sf0403054589 4 3058985 3.00E-07 NA
vg0122149418 sf0122148373 1 22149418 1.46E-06 9.48E-06